From 4f3f88630365aaebdacb93c1e42c33e34790d944 Mon Sep 17 00:00:00 2001 From: fmalmeida Date: Sun, 15 Jan 2023 15:53:31 +0100 Subject: [PATCH 01/32] Update plasmid_function.py --- falmeida_py/plasmid_function.py | 20 +++++++++++--------- 1 file changed, 11 insertions(+), 9 deletions(-) diff --git a/falmeida_py/plasmid_function.py b/falmeida_py/plasmid_function.py index aab1e37..3f7b838 100644 --- a/falmeida_py/plasmid_function.py +++ b/falmeida_py/plasmid_function.py @@ -42,15 +42,17 @@ def plasmids_stats(bacannot_summary): bacannot_summary[sample]['plasmid']['platon']['total'] = total_number # per plasmid info - for seq in [x for x in results['ID'].unique()]: - bacannot_summary[sample]['plasmid']['platon'][seq] = {} - bacannot_summary[sample]['plasmid']['platon'][seq]['Length'] = results.loc[results['ID'] == seq, 'Length'].item() - bacannot_summary[sample]['plasmid']['platon'][seq]['ORFs'] = results.loc[results['ID'] == seq, '# ORFs'].item() - bacannot_summary[sample]['plasmid']['platon'][seq]['Circular'] = results.loc[results['ID'] == seq, 'Circular'].item() - bacannot_summary[sample]['plasmid']['platon'][seq]['AMRs'] = results.loc[results['ID'] == seq, '# AMRs'].item() - bacannot_summary[sample]['plasmid']['platon'][seq]['Replication'] = results.loc[results['ID'] == seq, '# Replication'].item() - bacannot_summary[sample]['plasmid']['platon'][seq]['Mobilization'] = results.loc[results['ID'] == seq, '# Mobilization'].item() - bacannot_summary[sample]['plasmid']['platon'][seq]['Conjugation'] = results.loc[results['ID'] == seq, '# Conjugation'].item() + bacannot_summary[sample]['plasmid']['platon'] = {} + if int(results.shape[0]) > 0: + for seq in [x for x in results['ID'].unique()]: + bacannot_summary[sample]['plasmid']['platon'][seq] = {} + bacannot_summary[sample]['plasmid']['platon'][seq]['Length'] = results.loc[results['ID'] == seq, 'Length'].item() + bacannot_summary[sample]['plasmid']['platon'][seq]['ORFs'] = results.loc[results['ID'] == seq, '# ORFs'].item() + bacannot_summary[sample]['plasmid']['platon'][seq]['Circular'] = results.loc[results['ID'] == seq, 'Circular'].item() + bacannot_summary[sample]['plasmid']['platon'][seq]['AMRs'] = results.loc[results['ID'] == seq, '# AMRs'].item() + bacannot_summary[sample]['plasmid']['platon'][seq]['Replication'] = results.loc[results['ID'] == seq, '# Replication'].item() + bacannot_summary[sample]['plasmid']['platon'][seq]['Mobilization'] = results.loc[results['ID'] == seq, '# Mobilization'].item() + bacannot_summary[sample]['plasmid']['platon'][seq]['Conjugation'] = results.loc[results['ID'] == seq, '# Conjugation'].item() # plasmidfinder if os.path.exists(f"{results_dir}/plasmids/plasmidfinder/results_tab.tsv"): From 12c845809dd91f7c8422a90df9a6f8620f081f24 Mon Sep 17 00:00:00 2001 From: fmalmeida Date: Sat, 21 Jan 2023 11:15:22 +0100 Subject: [PATCH 02/32] Update __main__.py --- falmeida_py/__main__.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/falmeida_py/__main__.py b/falmeida_py/__main__.py index be6003d..85208f7 100644 --- a/falmeida_py/__main__.py +++ b/falmeida_py/__main__.py @@ -148,8 +148,8 @@ def main(): print(f"Processing file: {args['--gbk']}!") gbk2fasta(gbk=args['--gbk']) blast(task='blastn', query=args['--fasta'], subject='tmp_gbk.fa', - culling=args['--culling_limit'], minid=args['--minid'], mincov=args['--mincov'], - out='out.blast', threads=1, twoway=None) + culling=args['--culling_limit'], minid=args['--minid'], mincov=args['--mincov'], + out='out.blast', threads=1, twoway=None) filtergbk(gbk=args['--gbk'], out=args['--out'], extension=int(args['--extension'])) # Clean dir From 33ef9af82597884006a5c6ba3aa7f42f31774b44 Mon Sep 17 00:00:00 2001 From: fmalmeida Date: Thu, 9 Feb 2023 16:50:01 +0100 Subject: [PATCH 03/32] release v1.0.0 --- conda.recipe/meta.yaml | 2 +- falmeida_py/bacannot2json.py | 33 ++++++++++++--------------------- falmeida_py/plasmid_function.py | 3 ++- falmeida_py/version.py | 2 +- 4 files changed, 16 insertions(+), 24 deletions(-) diff --git a/conda.recipe/meta.yaml b/conda.recipe/meta.yaml index ff18464..de3fbe2 100644 --- a/conda.recipe/meta.yaml +++ b/conda.recipe/meta.yaml @@ -1,6 +1,6 @@ package: name: falmeida-py - version: '0.9' + version: '1.0.0' source: path: .. diff --git a/falmeida_py/bacannot2json.py b/falmeida_py/bacannot2json.py index 80a342a..532323b 100644 --- a/falmeida_py/bacannot2json.py +++ b/falmeida_py/bacannot2json.py @@ -41,29 +41,20 @@ ############################## ### fix keys in dictionary ### ############################## +def convert_dictkey(d): + ###change all keys in a dict d + return { str(k): convert_dictvalue(v) for k,v in d.items() } + +def convert_dictvalue(v): + ###if v is a dict do convert_dictkey() for v, else raise v + if isinstance(v, dict): + return convert_dictkey(v) + else: + return v + def stringify_keys(d): """Convert a dict's keys to strings if they are not.""" - for key in d.keys(): - - # check inner dict - if isinstance(d[key], dict): - value = stringify_keys(d[key]) - else: - value = d[key] - - # convert nonstring to string if needed - if not isinstance(key, str): - try: - d[str(key)] = value - except Exception: - try: - d[repr(key)] = value - except Exception: - raise - - # delete old key - del d[key] - return d + return convert_dictkey(d) ############################################### ### based on annotations figure sample name ### diff --git a/falmeida_py/plasmid_function.py b/falmeida_py/plasmid_function.py index 3f7b838..741549f 100644 --- a/falmeida_py/plasmid_function.py +++ b/falmeida_py/plasmid_function.py @@ -82,8 +82,9 @@ def plasmids_stats(bacannot_summary): bacannot_summary[sample]['plasmid']['plasmidfinder'][seq]['inc_types'] = {} bacannot_summary[sample]['plasmid']['plasmidfinder'][seq]['identity'] = {} bacannot_summary[sample]['plasmid']['plasmidfinder'][seq]['accession'] = {} + for index, row in results.iterrows(): - contig = row['Contig'] + contig = str(row['Contig']) bacannot_summary[sample]['plasmid']['plasmidfinder'][contig]['inc_types'] = row['Plasmid'] bacannot_summary[sample]['plasmid']['plasmidfinder'][contig]['identity'] = row['Identity'] bacannot_summary[sample]['plasmid']['plasmidfinder'][contig]['accession'] = row['Accession number'] \ No newline at end of file diff --git a/falmeida_py/version.py b/falmeida_py/version.py index 5a92447..8a005e5 100644 --- a/falmeida_py/version.py +++ b/falmeida_py/version.py @@ -14,7 +14,7 @@ If not, see . """ -__version__ = '0.9' +__version__ = '1.0.0' def get_version(): return __version__ From c9c3ba2f0de428ef64e97313eb0d8f9656cc3986 Mon Sep 17 00:00:00 2001 From: fmalmeida Date: Mon, 27 Feb 2023 17:01:19 +0100 Subject: [PATCH 04/32] fix indentation --- setup.py | 32 +++++++++++++++++--------------- 1 file changed, 17 insertions(+), 15 deletions(-) diff --git a/setup.py b/setup.py index 0535747..7b2d7ed 100644 --- a/setup.py +++ b/setup.py @@ -30,18 +30,20 @@ def readme(): with open('requirements.txt') as f: required = f.read().splitlines() -setup(name='falmeida-py', - version=__version__, - description='falmeida-py: a package to the simple distribution of my custom scripts.', - long_description=readme(), - long_description_content_type='text/markdown', - url='https://github.com/fmalmeida/pythonScripts', - author='Felipe Almeida', - author_email='almeidafmarques@gmail.com', - license='GPLv3', - packages=['falmeida_py'], - install_requires=required, - entry_points={"console_scripts": ['falmeida-py = falmeida_py.__main__:main']}, - include_package_data=True, - zip_safe=False, - python_requires='>=3.6') +setup( + name='falmeida-py', + version=__version__, + description='falmeida-py: a package to the simple distribution of my custom scripts.', + long_description=readme(), + long_description_content_type='text/markdown', + url='https://github.com/fmalmeida/pythonScripts', + author='Felipe Almeida', + author_email='almeidafmarques@gmail.com', + license='GPLv3', + packages=['falmeida_py'], + install_requires=required, + entry_points={"console_scripts": ['falmeida-py = falmeida_py.__main__:main']}, + include_package_data=True, + zip_safe=False, + python_requires='>=3.6' +) From a883d04abc4b36fcfb49afde78d7b44f766546ec Mon Sep 17 00:00:00 2001 From: fmalmeida Date: Mon, 27 Feb 2023 17:01:47 +0100 Subject: [PATCH 05/32] update version --- conda.recipe/meta.yaml | 2 +- falmeida_py/version.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/conda.recipe/meta.yaml b/conda.recipe/meta.yaml index de3fbe2..b16d576 100644 --- a/conda.recipe/meta.yaml +++ b/conda.recipe/meta.yaml @@ -1,6 +1,6 @@ package: name: falmeida-py - version: '1.0.0' + version: '1.1.0' source: path: .. diff --git a/falmeida_py/version.py b/falmeida_py/version.py index 8a005e5..73273b3 100644 --- a/falmeida_py/version.py +++ b/falmeida_py/version.py @@ -14,7 +14,7 @@ If not, see . """ -__version__ = '1.0.0' +__version__ = '1.1.0' def get_version(): return __version__ From d9f0c5d63f0215dc55a48b2a1501b35b45b6cc02 Mon Sep 17 00:00:00 2001 From: fmalmeida Date: Mon, 27 Feb 2023 17:58:28 +0100 Subject: [PATCH 06/32] add integron finder results to JSON --- bacannot_summary.json | 11492 ++++++++++++++++++++++++++++++ falmeida_py/bacannot2json.py | 4 + falmeida_py/mges_function.py | 59 + falmeida_py/plasmid_function.py | 4 - 4 files changed, 11555 insertions(+), 4 deletions(-) create mode 100644 bacannot_summary.json create mode 100644 falmeida_py/mges_function.py diff --git a/bacannot_summary.json b/bacannot_summary.json new file mode 100644 index 0000000..43bc050 --- /dev/null +++ b/bacannot_summary.json @@ -0,0 +1,11492 @@ +{ + "ecoli_1": { + "MGE": {}, + "general_annotation": { + "cds": 4681, + "closest_reference": { + "accession": "NZ_JTDT", + "distance": 0.00274861, + "strain": "Escherichia coli" + }, + "mlst": "73", + "rrna": 4, + "tmrna": 1, + "trna": 70 + }, + "plasmid": { + "plasmidfinder": {}, + "platon": { + "84": { + "AMRs": 0, + "Circular": "no", + "Conjugation": 0, + "Length": 10558, + "Mobilization": 0, + "ORFs": 5, + "Replication": 0 + } + } + }, + "resistance": { + "amrfinderplus": { + "GOMEMAFE_00009": { + "card_aro": 3000502, + "contig": 1, + "end": 8462, + "gene": "acrF", + "identity": 99.42, + "start": 5358, + "subclass": "EFFLUX", + "type": "AMR" + }, + "GOMEMAFE_00892": { + "card_aro": null, + "contig": 6, + "end": 72884, + "gene": "fieF", + "identity": 99.67, + "start": 71982, + "subclass": null, + "type": "STRESS" + }, + "GOMEMAFE_01968": { + "card_aro": null, + "contig": 17, + "end": 8615, + "gene": "ymgB", + "identity": 97.73, + "start": 8349, + "subclass": null, + "type": "STRESS" + }, + "GOMEMAFE_02188": { + "card_aro": null, + "contig": 20, + "end": 8779, + "gene": "asr", + "identity": 98.04, + "start": 8471, + "subclass": null, + "type": "STRESS" + }, + "GOMEMAFE_02315": { + "card_aro": null, + "contig": 21, + "end": 64895, + "gene": "emrD", + "identity": 99.49, + "start": 63711, + "subclass": "EFFLUX", + "type": "AMR" + }, + "GOMEMAFE_02346": { + "card_aro": 3004039, + "contig": 22, + "end": 15190, + "gene": "emrE", + "identity": 98.18, + "start": 14858, + "subclass": "EFFLUX", + "type": "STRESS" + }, + "GOMEMAFE_02841": { + "card_aro": 3006880, + "contig": 28, + "end": 57085, + "gene": "blaEC-5", + "identity": 100.0, + "start": 55952, + "subclass": "CEPHALOSPORIN", + "type": "AMR" + }, + "GOMEMAFE_03475": { + "card_aro": null, + "contig": 40, + "end": 27348, + "gene": "arsC", + "identity": 93.62, + "start": 26923, + "subclass": "ARSENATE", + "type": "STRESS" + }, + "total": 8 + }, + "resfinder": { + "total": 0 + }, + "rgi": { + "GOMEMAFE_00009": { + "accession": 1437, + "card_aro": 3000502, + "contig": 1, + "cut_off": "Strict", + "end": 8462, + "gene": "AcrF", + "gene_family": "resistance-nodulation-cell division (RND) antibiotic efflux pump", + "identity": 99.42, + "name": "Multidrug export protein AcrF", + "resistance_mechanism": "antibiotic efflux", + "start": 5358, + "subclass": "fluoroquinolone antibiotic; cephalosporin; cephamycin; penam" + }, + "GOMEMAFE_00010": { + "accession": 1445, + "card_aro": 3000499, + "contig": 1, + "cut_off": "Strict", + "end": 9631, + "gene": "AcrE", + "gene_family": "resistance-nodulation-cell division (RND) antibiotic efflux pump", + "identity": 99.48, + "name": "Multidrug export protein AcrE", + "resistance_mechanism": "antibiotic efflux", + "start": 8474, + "subclass": "fluoroquinolone antibiotic; cephalosporin; cephamycin; penam" + }, + "GOMEMAFE_00011": { + "accession": 520, + "card_aro": 3000656, + "contig": 1, + "cut_off": "Strict", + "end": 10692, + "gene": "AcrS", + "gene_family": "resistance-nodulation-cell division (RND) antibiotic efflux pump", + "identity": 98.18, + "name": "HTH-type transcriptional regulator AcrR", + "resistance_mechanism": "antibiotic efflux", + "start": 10030, + "subclass": "fluoroquinolone antibiotic; cephalosporin; glycylcycline; cephamycin; penam; tetracycline antibiotic; rifamycin antibiotic; phenicol antibiotic; disinfecting agents and antiseptics" + }, + "GOMEMAFE_00231": { + "accession": 1427, + "card_aro": 3000491, + "contig": 2, + "cut_off": "Strict", + "end": 47007, + "gene": "acrD", + "gene_family": "resistance-nodulation-cell division (RND) antibiotic efflux pump", + "identity": 99.71, + "name": "Multidrug efflux pump subunit AcrB", + "resistance_mechanism": "antibiotic efflux", + "start": 43894, + "subclass": "aminoglycoside antibiotic" + }, + "GOMEMAFE_00318": { + "accession": 1318, + "card_aro": 3000833, + "contig": 2, + "cut_off": "Strict", + "end": 138605, + "gene": "evgS", + "gene_family": "major facilitator superfamily (MFS) antibiotic efflux pump; resistance-nodulation-cell division (RND) antibiotic efflux pump", + "identity": 96.66, + "name": "Sensor protein EvgS", + "resistance_mechanism": "antibiotic efflux", + "start": 135012, + "subclass": "macrolide antibiotic; fluoroquinolone antibiotic; penam; tetracycline antibiotic" + }, + "GOMEMAFE_00319": { + "accession": 1015, + "card_aro": 3000832, + "contig": 2, + "cut_off": "Perfect", + "end": 139224, + "gene": "evgA", + "gene_family": "major facilitator superfamily (MFS) antibiotic efflux pump; resistance-nodulation-cell division (RND) antibiotic efflux pump", + "identity": 100.0, + "name": "DNA-binding transcriptional activator EvgA", + "resistance_mechanism": "antibiotic efflux", + "start": 138610, + "subclass": "macrolide antibiotic; fluoroquinolone antibiotic; penam; tetracycline antibiotic" + }, + "GOMEMAFE_00320": { + "accession": 609, + "card_aro": 3000206, + "contig": 2, + "cut_off": "Strict", + "end": 140803, + "gene": "emrK", + "gene_family": "major facilitator superfamily (MFS) antibiotic efflux pump", + "identity": 98.86, + "name": "putative multidrug resistance protein EmrK", + "resistance_mechanism": "antibiotic efflux", + "start": 139640, + "subclass": "tetracycline antibiotic" + }, + "GOMEMAFE_00321": { + "accession": 540, + "card_aro": 3000254, + "contig": 2, + "cut_off": "Strict", + "end": 142341, + "gene": "emrY", + "gene_family": "major facilitator superfamily (MFS) antibiotic efflux pump", + "identity": 99.8, + "name": "putative multidrug resistance protein EmrY", + "resistance_mechanism": "antibiotic efflux", + "start": 140803, + "subclass": "tetracycline antibiotic" + }, + "GOMEMAFE_00431": { + "accession": 1330, + "card_aro": 3000516, + "contig": 3, + "cut_off": "Perfect", + "end": 51266, + "gene": "emrR", + "gene_family": "major facilitator superfamily (MFS) antibiotic efflux pump", + "identity": 100.0, + "name": "Transcriptional repressor MprA", + "resistance_mechanism": "antibiotic efflux", + "start": 50736, + "subclass": "fluoroquinolone antibiotic" + }, + "GOMEMAFE_00432": { + "accession": 1757, + "card_aro": 3000027, + "contig": 3, + "cut_off": "Strict", + "end": 52565, + "gene": "emrA", + "gene_family": "major facilitator superfamily (MFS) antibiotic efflux pump", + "identity": 99.74, + "name": "Multidrug export protein EmrA", + "resistance_mechanism": "antibiotic efflux", + "start": 51393, + "subclass": "fluoroquinolone antibiotic" + }, + "GOMEMAFE_00433": { + "accession": 1847, + "card_aro": 3000074, + "contig": 3, + "cut_off": "Strict", + "end": 54120, + "gene": "emrB", + "gene_family": "major facilitator superfamily (MFS) antibiotic efflux pump", + "identity": 99.8, + "name": "Multidrug export protein EmrB", + "resistance_mechanism": "antibiotic efflux", + "start": 52582, + "subclass": "fluoroquinolone antibiotic" + }, + "GOMEMAFE_00739": { + "accession": 2424, + "card_aro": 3003952, + "contig": 5, + "cut_off": "Strict", + "end": 24184, + "gene": "YojI", + "gene_family": "ATP-binding cassette (ABC) antibiotic efflux pump", + "identity": 99.63, + "name": "ABC transporter ATP-binding/permease protein YojI", + "resistance_mechanism": "antibiotic efflux", + "start": 22541, + "subclass": "peptide antibiotic" + }, + "GOMEMAFE_00766": { + "accession": 2372, + "card_aro": 3003889, + "contig": 5, + "cut_off": "Strict", + "end": 66818, + "gene": "Escherichia coli GlpT with mutation conferring resistance to fosfomycin", + "gene_family": "antibiotic-resistant GlpT", + "identity": 99.52, + "name": "Glycerol-3-phosphate transporter", + "resistance_mechanism": "antibiotic target alteration", + "start": 66195, + "subclass": "phosphonic acid antibiotic" + }, + "GOMEMAFE_00781": { + "accession": 2014, + "card_aro": 3003578, + "contig": 5, + "cut_off": "Strict", + "end": 83047, + "gene": "PmrF", + "gene_family": "pmr phosphoethanolamine transferase", + "identity": 99.38, + "name": "Undecaprenyl-phosphate 4-deoxy-4-formamido-L-arabinose transferase", + "resistance_mechanism": "antibiotic target alteration", + "start": 82079, + "subclass": "peptide antibiotic" + }, + "GOMEMAFE_00895": { + "accession": 152, + "card_aro": 3000830, + "contig": 6, + "cut_off": "Perfect", + "end": 75751, + "gene": "cpxA", + "gene_family": "resistance-nodulation-cell division (RND) antibiotic efflux pump", + "identity": 100.0, + "name": "Sensor histidine kinase CpxA", + "resistance_mechanism": "antibiotic efflux", + "start": 74378, + "subclass": "aminoglycoside antibiotic; aminocoumarin antibiotic" + }, + "GOMEMAFE_01051": { + "accession": 826, + "card_aro": 3000237, + "contig": 7, + "cut_off": "Strict", + "end": 107908, + "gene": "TolC", + "gene_family": "ATP-binding cassette (ABC) antibiotic efflux pump; major facilitator superfamily (MFS) antibiotic efflux pump; resistance-nodulation-cell division (RND) antibiotic efflux pump", + "identity": 99.59, + "name": "Outer membrane protein TolC", + "resistance_mechanism": "antibiotic efflux", + "start": 106427, + "subclass": "macrolide antibiotic; fluoroquinolone antibiotic; aminoglycoside antibiotic; carbapenem; cephalosporin; glycylcycline; cephamycin; penam; tetracycline antibiotic; peptide antibiotic; aminocoumarin antibiotic; rifamycin antibiotic; phenicol antibiotic; penem; disinfecting agents and antiseptics" + }, + "GOMEMAFE_01431": { + "accession": 2423, + "card_aro": 3003950, + "contig": 11, + "cut_off": "Strict", + "end": 51647, + "gene": "msbA", + "gene_family": "ATP-binding cassette (ABC) antibiotic efflux pump", + "identity": 99.66, + "name": "Lipid A export ATP-binding/permease protein MsbA", + "resistance_mechanism": "antibiotic efflux", + "start": 49899, + "subclass": "nitroimidazole antibiotic" + }, + "GOMEMAFE_01545": { + "accession": 37, + "card_aro": 3001328, + "contig": 12, + "cut_off": "Strict", + "end": 57024, + "gene": "Escherichia coli mdfA", + "gene_family": "major facilitator superfamily (MFS) antibiotic efflux pump", + "identity": 97.07, + "name": "Multidrug transporter MdfA", + "resistance_mechanism": "antibiotic efflux", + "start": 55792, + "subclass": "tetracycline antibiotic; disinfecting agents and antiseptics" + }, + "GOMEMAFE_01662": { + "accession": 2066, + "card_aro": 3003511, + "contig": 13, + "cut_off": "Strict", + "end": 85591, + "gene": "Escherichia coli soxS with mutation conferring antibiotic resistance", + "gene_family": "ATP-binding cassette (ABC) antibiotic efflux pump; major facilitator superfamily (MFS) antibiotic efflux pump; resistance-nodulation-cell division (RND) antibiotic efflux pump; General Bacterial Porin with reduced permeability to beta-lactams", + "identity": 100.0, + "name": "Regulatory protein SoxS", + "resistance_mechanism": "antibiotic target alteration; antibiotic efflux; reduced permeability to antibiotic", + "start": 85268, + "subclass": "fluoroquinolone antibiotic; monobactam; carbapenem; cephalosporin; glycylcycline; cephamycin; penam; tetracycline antibiotic; rifamycin antibiotic; phenicol antibiotic; penem; disinfecting agents and antiseptics" + }, + "GOMEMAFE_01663": { + "accession": 1005, + "card_aro": 3003381, + "contig": 13, + "cut_off": "Strict", + "end": 86141, + "gene": "Escherichia coli soxR with mutation conferring antibiotic resistance", + "gene_family": "ATP-binding cassette (ABC) antibiotic efflux pump; major facilitator superfamily (MFS) antibiotic efflux pump; resistance-nodulation-cell division (RND) antibiotic efflux pump", + "identity": 99.35, + "name": "Redox-sensitive transcriptional activator SoxR", + "resistance_mechanism": "antibiotic target alteration; antibiotic efflux", + "start": 85677, + "subclass": "fluoroquinolone antibiotic; cephalosporin; glycylcycline; penam; tetracycline antibiotic; rifamycin antibiotic; phenicol antibiotic; disinfecting agents and antiseptics" + }, + "GOMEMAFE_01771": { + "accession": 2331, + "card_aro": 3003841, + "contig": 14, + "cut_off": "Strict", + "end": 92341, + "gene": "kdpE", + "gene_family": "kdpDE", + "identity": 99.55, + "name": "KDP operon transcriptional regulatory protein KdpE", + "resistance_mechanism": "antibiotic efflux", + "start": 91664, + "subclass": "aminoglycoside antibiotic" + }, + "GOMEMAFE_01889": { + "accession": 869, + "card_aro": 3000518, + "contig": 16, + "cut_off": "Strict", + "end": 15657, + "gene": "CRP", + "gene_family": "resistance-nodulation-cell division (RND) antibiotic efflux pump", + "identity": 99.52, + "name": "cAMP-activated global transcriptional regulator CRP", + "resistance_mechanism": "antibiotic efflux", + "start": 15025, + "subclass": "macrolide antibiotic; fluoroquinolone antibiotic; penam" + }, + "GOMEMAFE_02050": { + "accession": 1248, + "card_aro": 3000676, + "contig": 17, + "cut_off": "Perfect", + "end": 90083, + "gene": "H-NS", + "gene_family": "major facilitator superfamily (MFS) antibiotic efflux pump; resistance-nodulation-cell division (RND) antibiotic efflux pump", + "identity": 100.0, + "name": "DNA-binding protein H-NS", + "resistance_mechanism": "antibiotic efflux", + "start": 89670, + "subclass": "macrolide antibiotic; fluoroquinolone antibiotic; cephalosporin; cephamycin; penam; tetracycline antibiotic" + }, + "GOMEMAFE_02223": { + "accession": 1922, + "card_aro": 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"DNA-binding_transcriptional_regulator_PhoP", + "product": "gi|24112549|ref|NP_707059.1|DNA-binding_transcriptional_regulator_PhoP_[Shigella_flexneri_2a_str._301]", + "start": 2119318 + }, + "FKEDNGPL_02109": { + "contig": "NZ_CP006659.2", + "end": 2219712, + "id": "16764663", + "name": "PTS_system_N,N'-diacetylchitobiose-specific_transporter_subunit_IIB", + "product": "gi|16764663|ref|NP_460278.1|PTS_system_N,N'-diacetylchitobiose-specific_transporter_subunit_IIB_[Salmonella_enterica_subsp._enterica_serovar_Typhimurium_str._LT2]", + "start": 2219392 + }, + "FKEDNGPL_02395": { + "contig": "NZ_CP006659.2", + "end": 2504021, + "id": "16766107", + "name": "transporter", + "product": "gi|16766107|ref|NP_461722.1|transporter_[Salmonella_enterica_subsp._enterica_serovar_Typhimurium_str._LT2]", + "start": 2503863 + }, + "FKEDNGPL_02920": { + "contig": "NZ_CP006659.2", + "end": 3033360, + "id": "24113046", + "name": "superoxide_dismutase", + "product": "gi|24113046|ref|NP_707556.1|superoxide_dismutase_[Shigella_flexneri_2a_str._301]", + "start": 3032779 + }, + "FKEDNGPL_03060": { + "contig": "NZ_CP006659.2", + "end": 3173089, + "id": "218929485", + "name": "major_outer_membrane_lipoprotein", + "product": "gi|218929485|ref|YP_002347360.1|major_outer_membrane_lipoprotein_[Yersinia_pestis_CO92]", + "start": 3172853 + }, + "FKEDNGPL_03132": { + "contig": "NZ_CP006659.2", + "end": 3248764, + "id": "24112632", + "name": "UTP-glucose-1-phosphate_uridylyltransferase", + "product": "gi|24112632|ref|NP_707142.1|UTP-glucose-1-phosphate_uridylyltransferase_[Shigella_flexneri_2a_str._301]", + "start": 3247862 + }, + "FKEDNGPL_03173": { + "contig": "NZ_CP006659.2", + "end": 3296054, + "id": "117623421", + "name": "GTP-dependent_nucleic_acid-binding_protein_EngD", + "product": "gi|117623421|ref|YP_852334.1|GTP-dependent_nucleic_acid-binding_protein_EngD_[Escherichia_coli_APEC_O1]", + "start": 3294963 + }, + "FKEDNGPL_03251": { + "contig": "NZ_CP006659.2", + "end": 3379910, + "id": "16765159", + "name": "long-chain-fatty-acid--CoA_ligase", + "product": "gi|16765159|ref|NP_460774.1|long-chain-fatty-acid--CoA_ligase_[Salmonella_enterica_subsp._enterica_serovar_Typhimurium_str._LT2]", + "start": 3378192 + }, + "FKEDNGPL_03269": { + "contig": "NZ_CP006659.2", + "end": 3398678, + "id": "15802236", + "name": "cold_shock-like_protein_CspC", + "product": "gi|15802236|ref|NP_288259.1|cold_shock-like_protein_CspC_[Escherichia_coli_O157:H7_str._EDL933]", + "start": 3398469 + }, + "FKEDNGPL_03303": { + "contig": "NZ_CP006659.2", + "end": 3434751, + "id": "39546331", + "name": "zinc_ABC_transporter_ATP-binding_protein_ZnuC", + "product": "gi|39546331|ref|NP_460849.2|zinc_ABC_transporter_ATP-binding_protein_ZnuC_[Salmonella_enterica_subsp._enterica_serovar_Typhimurium_str._LT2]", + "start": 3433999 + }, + "FKEDNGPL_03304": { + "contig": "NZ_CP006659.2", + "end": 3435536, + "id": "16765235", + "name": "zinc_ABC_transporter_permease_ZnuB", + "product": "gi|16765235|ref|NP_460850.1|zinc_ABC_transporter_permease_ZnuB_[Salmonella_enterica_subsp._enterica_serovar_Typhimurium_str._LT2]", + "start": 3434751 + }, + "FKEDNGPL_03342": { + "contig": "NZ_CP006659.2", + "end": 3471454, + "id": "16765285", + "name": "LuxR/UhpA_family_response_regulator", + "product": "gi|16765285|ref|NP_460900.1|LuxR/UhpA_family_response_regulator_[Salmonella_enterica_subsp._enterica_serovar_Typhimurium_str._LT2]", + "start": 3470798 + }, + "FKEDNGPL_03445": { + "contig": "NZ_CP006659.2", + "end": 3579164, + "id": "16765428", + "name": "UTP--glucose-1-phosphate_uridylyltransferase_subunit_GalF", + "product": "gi|16765428|ref|NP_461043.1|UTP--glucose-1-phosphate_uridylyltransferase_subunit_GalF_[Salmonella_enterica_subsp._enterica_serovar_Typhimurium_str._LT2]", + "start": 3578316 + }, + "FKEDNGPL_03499": { + "contig": "NZ_CP006659.2", + "end": 3636422, + "id": "16765465", + "name": "protease", + "product": "gi|16765465|ref|NP_461080.1|protease_[Salmonella_enterica_subsp._enterica_serovar_Typhimurium_str._LT2]", + "start": 3635061 + }, + "FKEDNGPL_03686": { + "contig": "NZ_CP006659.2", + "end": 3850710, + "id": "16761308", + "name": "chorismate_synthase", + "product": "gi|16761308|ref|NP_456925.1|chorismate_synthase_[Salmonella_enterica_subsp._enterica_serovar_Typhi_str._CT18]", + "start": 3849625 + }, + "FKEDNGPL_03792": { + "contig": "NZ_CP006659.2", + "end": 3959792, + "id": "16765821", + "name": "polyphosphate_kinase", + "product": "gi|16765821|ref|NP_461436.1|polyphosphate_kinase_[Salmonella_enterica_subsp._enterica_serovar_Typhimurium_str._LT2]", + "start": 3957732 + }, + "FKEDNGPL_03853": { + "contig": "NZ_CP006659.2", + "end": 4011931, + "id": "24113836", + "name": "GMP_synthase", + "product": "gi|24113836|ref|NP_708346.1|GMP_synthase_[Shigella_flexneri_2a_str._301]", + "start": 4010354 + }, + "FKEDNGPL_03854": { + "contig": "NZ_CP006659.2", + "end": 4013465, + "id": "56480121", + "name": "inosine_5'-monophosphate_dehydrogenase", + "product": "gi|56480121|ref|NP_708347.2|inosine_5'-monophosphate_dehydrogenase_[Shigella_flexneri_2a_str._301]", + "start": 4011999 + }, + "FKEDNGPL_03903": { + "contig": "NZ_CP006659.2", + "end": 4073409, + "id": "16765896", + "name": "ferredoxin", + "product": "gi|16765896|ref|NP_461511.1|ferredoxin_[Salmonella_enterica_subsp._enterica_serovar_Typhimurium_str._LT2]", + "start": 4073149 + }, + "FKEDNGPL_03932": { + "contig": "NZ_CP006659.2", + "end": 4105356, + "id": "16765976", + "name": "chaperone_protein_ClpB", + "product": "gi|16765976|ref|NP_461591.1|chaperone_protein_ClpB_[Salmonella_enterica_subsp._enterica_serovar_Typhimurium_str._LT2]", + "start": 4102783 + }, + "FKEDNGPL_04406": { + "contig": "NZ_CP006659.2", + "end": 4580961, + "id": "15803477", + "name": "arginine_decarboxylase", + "product": "gi|15803477|ref|NP_289510.1|arginine_decarboxylase_[Escherichia_coli_O157:H7_str._EDL933]", + "start": 4578985 + }, + "FKEDNGPL_04717": { + "contig": "NZ_CP006659.2", + "end": 4884708, + "id": "16766637", + "name": "stringent_starvation_protein_A", + "product": "gi|16766637|ref|NP_462252.1|stringent_starvation_protein_A_[Salmonella_enterica_subsp._enterica_serovar_Typhimurium_str._LT2]", + "start": 4884070 + }, + "FKEDNGPL_04846": { + "contig": "NZ_CP006659.2", + "end": 4989716, + "id": "16766754", + "name": "cAMP-activated_global_transcriptional_regulator", + "product": "gi|16766754|ref|NP_462369.1|cAMP-activated_global_transcriptional_regulator_[Salmonella_enterica_subsp._enterica_serovar_Typhimurium_str._LT2]", + "start": 4989084 + }, + "FKEDNGPL_04877": { + "contig": "NZ_CP006659.2", + "end": 5023818, + "id": "16766789", + "name": "osmolarity_sensor_protein_EnvZ", + "product": "gi|16766789|ref|NP_462404.1|osmolarity_sensor_protein_EnvZ_[Salmonella_enterica_subsp._enterica_serovar_Typhimurium_str._LT2]", + "start": 5022463 + }, + "FKEDNGPL_04878": { + "contig": "NZ_CP006659.2", + "end": 5024534, + "id": "56480330", + "name": "osmolarity_response_regulator", + "product": "gi|56480330|ref|NP_709178.2|osmolarity_response_regulator_[Shigella_flexneri_2a_str._301]", + "start": 5023815 + }, + "FKEDNGPL_05003": { + "contig": "NZ_CP006659.2", + "end": 5176986, + "id": "117625828", + "name": "dipeptide_transporter_protein_DppA", + "product": "gi|117625828|ref|YP_859151.1|dipeptide_transporter_protein_DppA_[Escherichia_coli_APEC_O1]", + "start": 5175379 + }, + "FKEDNGPL_05102": { + "contig": "NZ_CP006659.2", + "end": 5282416, + "id": "22124023", + "name": "bifunctional_(p)ppGpp_synthetase_II/_guanosine-3',5'-bis_pyrophosphate_3'-pyrophosphohydrolase", + "product": "gi|22124023|ref|NP_667446.1|bifunctional_(p)ppGpp_synthetase_II/_guanosine-3',5'-bis_pyrophosphate_3'-pyrophosphohydrolase_[Yersinia_pestis_KIM10+]", + "start": 5280296 + }, + "FKEDNGPL_05198": { + "contig": "NZ_CP006659.2", + "end": 5381601, + "id": "228960701", + "name": "heat_shock_protein_IbpA", + "product": "gi|228960701|ref|NP_462709.3|heat_shock_protein_IbpA_[Salmonella_enterica_subsp._enterica_serovar_Typhimurium_str._LT2]", + "start": 5381188 + }, + "total": 53 + } + } + } +} \ No newline at end of file diff --git a/falmeida_py/bacannot2json.py b/falmeida_py/bacannot2json.py index 532323b..b4a8b75 100644 --- a/falmeida_py/bacannot2json.py +++ b/falmeida_py/bacannot2json.py @@ -37,6 +37,7 @@ from .plasmid_function import * from .virulence_function import * from .resistance_function import * +from .mges_function import * ############################## ### fix keys in dictionary ### @@ -103,6 +104,9 @@ def bacannot2json(indir, outfile, check): # check virulence annotation stats virulence_stats( bacannot_summary ) + # check MGEs annotation stats + mges_stats( bacannot_summary ) + # check plasmids annotation stats plasmids_stats( bacannot_summary ) diff --git a/falmeida_py/mges_function.py b/falmeida_py/mges_function.py new file mode 100644 index 0000000..29d1c46 --- /dev/null +++ b/falmeida_py/mges_function.py @@ -0,0 +1,59 @@ +################################## +### Loading Necessary Packages ### +################################## +import pandas as pd +import os + +#################################### +### check MGEs annotations stats ### +#################################### +def mges_stats(bacannot_summary): + + # iterate over available samples + for sample in bacannot_summary: + + # load dir of samples' results + results_dir = bacannot_summary[sample]['results_dir'] + + # init MGE annotation dictionary + bacannot_summary[sample]['MGE'] = {} + + # load annotation stats + if os.path.exists(f"{results_dir}/integron_finder"): + + # integron_finder + if os.path.exists(f"{results_dir}/integron_finder/{sample}_integrons.gff"): + + # init integron_finder annotation dictionary + bacannot_summary[sample]['MGE']['integron_finder'] = {} + + # load integron_finder results + results = pd.read_csv( + f"{results_dir}/integron_finder/{sample}_integrons.gff", + sep='\t', + header=None, + names=[ + 'chr', 'source', 'type', 'start', 'end', 'score', 'strand', 'frame', 'atts' + ] + ) + + # number of integron_finder annotations + total_number = len(results.index) + bacannot_summary[sample]['MGE']['integron_finder']['total'] = total_number + + # per integron info + bacannot_summary[sample]['MGE']['integron_finder'] = {} + if int(results.shape[0]) > 0: + for seq in [ str(x) for x in results['chr'].unique() ]: + + bacannot_summary[sample]['MGE']['integron_finder'][seq] = {} + for index, row in results[results['chr'] == seq].reset_index().iterrows(): + id = row['atts'].split(';')[0].split('=')[-1] + bacannot_summary[sample]['MGE']['integron_finder'][seq][id] = {} + bacannot_summary[sample]['MGE']['integron_finder'][seq][id]['id'] = id + bacannot_summary[sample]['MGE']['integron_finder'][seq][id]['contig'] = row['chr'] + bacannot_summary[sample]['MGE']['integron_finder'][seq][id]['start'] = row['start'] + bacannot_summary[sample]['MGE']['integron_finder'][seq][id]['end'] = row['end'] + bacannot_summary[sample]['MGE']['integron_finder'][seq][id]['type'] = row['atts'].split(';')[1].split('=')[-1] + bacannot_summary[sample]['MGE']['integron_finder'][seq][id]['source'] = row['source'] + bacannot_summary[sample]['MGE']['integron_finder'][seq][id]['product'] = row['type'] \ No newline at end of file diff --git a/falmeida_py/plasmid_function.py b/falmeida_py/plasmid_function.py index 741549f..86e00a8 100644 --- a/falmeida_py/plasmid_function.py +++ b/falmeida_py/plasmid_function.py @@ -2,11 +2,7 @@ ### Loading Necessary Packages ### ################################## import pandas as pd -from .utils import find_files -import json import os -import yaml -from pathlib import Path ######################################## ### check plasmids annotations stats ### From 618cd3ec87e5866b28b29bdd3e335916b3a9889d Mon Sep 17 00:00:00 2001 From: fmalmeida Date: Mon, 27 Feb 2023 18:47:49 +0100 Subject: [PATCH 07/32] update package --- docs/align2subsetgbk_help.txt | 50 +++++------------------------------ docs/help_message.txt | 31 +++++----------------- docs/splitgbk_help.txt | 44 +++++------------------------- docs/tsv2markdown_help.txt | 46 +++++--------------------------- 4 files changed, 24 insertions(+), 147 deletions(-) diff --git a/docs/align2subsetgbk_help.txt b/docs/align2subsetgbk_help.txt index 769c2b2..087e990 100644 --- a/docs/align2subsetgbk_help.txt +++ b/docs/align2subsetgbk_help.txt @@ -1,44 +1,6 @@ -A script meant to subset a genbank annotation file based on alignments against a query (Nucleotide) FASTA file - ---- -Copyright (C) 2020 Felipe Marques de Almeida (almeidafmarques@gmail.com) -License: Public Domain - -Usage: - falmeida-py align2subsetgbk [ -h|--help ] - falmeida-py align2subsetgbk [ --gbk --fasta --out --minid --mincov --culling_limit --extension ] - -Options: - -h --help Show this screen. - -g --gbk= Gbk file for subset - -f --fasta= FASTA (nucl) file for querying the gbk - -o --out= Gbk filtered output file [Default: out.gbk]. - --extension= Base pair length to extend the flank regions in the alignment [Default: 0]. - --minid= Min. Identity percentage for gene annotation [Default: 80]. - --mincov= Min. Covereage for gene annotation [Default: 80]. - --culling_limit= Blast culling_limit for best hit only [Default: 1]. -falmeida-py: a package to the simple distribution of my custom scripts. - -Copyright (C) 2020 Felipe Marques de Almeida (almeidafmarques@gmail.com) -License: Public Domain - -usage: - falmeida-py [ -h|--help ] [ -v|--version ] [ --license ] - falmeida-py [ -h|--help ] [ ... ] - -options: - -h --help Show this screen - -v --version Show version information - --license Show LEGAL LICENSE information - -commands: - tsv2markdown Command for rapid convertion of tsv or csv to markdown tables. - splitgbk Command to split multisequence genbank files into individual files. - align2subsetgbk Command to subset genbank files based on alignments to a FASTA file. - gbk2fasta Command to convert genbank files to fasta files. - blasts Command to execute automatized blast commands. - replace_fasta_seq Command to replace strings in a FASTA using defitinitions from a BED file - mpgap2csv Command to summarize main mpgap multiqc assembly statistics into a CSV file - bacannot2json Command to summarize main bacannot annotation results into JSON file - -Use: `falmeida-py -h` to get more help and see examples. +Traceback (most recent call last): + File "/home/falmeida/Documents/GitHub/pythonScripts/falmeida-py-runner.py", line 18, in + from falmeida_py.__main__ import main + File "/home/falmeida/Documents/GitHub/pythonScripts/falmeida_py/__main__.py", line 47, in + from docopt import docopt +ModuleNotFoundError: No module named 'docopt' diff --git a/docs/help_message.txt b/docs/help_message.txt index 6ed5318..087e990 100644 --- a/docs/help_message.txt +++ b/docs/help_message.txt @@ -1,25 +1,6 @@ -falmeida-py: a package to the simple distribution of my custom scripts. - -Copyright (C) 2020 Felipe Marques de Almeida (almeidafmarques@gmail.com) -License: Public Domain - -usage: - falmeida-py [ -h|--help ] [ -v|--version ] [ --license ] - falmeida-py [ -h|--help ] [ ... ] - -options: - -h --help Show this screen - -v --version Show version information - --license Show LEGAL LICENSE information - -commands: - tsv2markdown Command for rapid convertion of tsv or csv to markdown tables. - splitgbk Command to split multisequence genbank files into individual files. - align2subsetgbk Command to subset genbank files based on alignments to a FASTA file. - gbk2fasta Command to convert genbank files to fasta files. - blasts Command to execute automatized blast commands. - replace_fasta_seq Command to replace strings in a FASTA using defitinitions from a BED file - mpgap2csv Command to summarize main mpgap multiqc assembly statistics into a CSV file - bacannot2json Command to summarize main bacannot annotation results into JSON file - -Use: `falmeida-py -h` to get more help and see examples. +Traceback (most recent call last): + File "/home/falmeida/Documents/GitHub/pythonScripts/falmeida-py-runner.py", line 18, in + from falmeida_py.__main__ import main + File "/home/falmeida/Documents/GitHub/pythonScripts/falmeida_py/__main__.py", line 47, in + from docopt import docopt +ModuleNotFoundError: No module named 'docopt' diff --git a/docs/splitgbk_help.txt b/docs/splitgbk_help.txt index f139033..087e990 100644 --- a/docs/splitgbk_help.txt +++ b/docs/splitgbk_help.txt @@ -1,38 +1,6 @@ -A very simple script to split multisequence genbank files into separate files -Copyright (C) 2020 Felipe Marques de Almeida (almeidafmarques@gmail.com) -License: Public Domain - -usage: - falmeida-py splitgbk - falmeida-py splitgbk [ -h|--help ] - falmeida-py splitgbk [ --gbk ] [ --outdir ] - -options: - -h --help Show this screen. - -g --gbk= Input genbank file to split into multiple individual files. - -o --outdir= Directory (must already exist) in which to write the splitted files [Default: ./]. -falmeida-py: a package to the simple distribution of my custom scripts. - -Copyright (C) 2020 Felipe Marques de Almeida (almeidafmarques@gmail.com) -License: Public Domain - -usage: - falmeida-py [ -h|--help ] [ -v|--version ] [ --license ] - falmeida-py [ -h|--help ] [ ... ] - -options: - -h --help Show this screen - -v --version Show version information - --license Show LEGAL LICENSE information - -commands: - tsv2markdown Command for rapid convertion of tsv or csv to markdown tables. - splitgbk Command to split multisequence genbank files into individual files. - align2subsetgbk Command to subset genbank files based on alignments to a FASTA file. - gbk2fasta Command to convert genbank files to fasta files. - blasts Command to execute automatized blast commands. - replace_fasta_seq Command to replace strings in a FASTA using defitinitions from a BED file - mpgap2csv Command to summarize main mpgap multiqc assembly statistics into a CSV file - bacannot2json Command to summarize main bacannot annotation results into JSON file - -Use: `falmeida-py -h` to get more help and see examples. +Traceback (most recent call last): + File "/home/falmeida/Documents/GitHub/pythonScripts/falmeida-py-runner.py", line 18, in + from falmeida_py.__main__ import main + File "/home/falmeida/Documents/GitHub/pythonScripts/falmeida_py/__main__.py", line 47, in + from docopt import docopt +ModuleNotFoundError: No module named 'docopt' diff --git a/docs/tsv2markdown_help.txt b/docs/tsv2markdown_help.txt index 0b2b685..087e990 100644 --- a/docs/tsv2markdown_help.txt +++ b/docs/tsv2markdown_help.txt @@ -1,40 +1,6 @@ -A simple script to convert tsv (or csv) files to markdown tables using tabulate! -Copyright (C) 2020 Felipe Marques de Almeida (almeidafmarques@gmail.com) -License: Public Domain - -usage: - falmeida-py tsv2markdown - falmeida-py tsv2markdown [ -h|--help ] - falmeida-py tsv2markdown [ --tsv --csv --header ] - -options: - -h --help Show this screen. - --tsv= Input tsv file to print as markdown table - --csv= Input csv file to print as markdown table - --header= If file does not have a header, set a - custom header. E.g. --header "Planet,R (km),mass (x 10^29 kg)". -falmeida-py: a package to the simple distribution of my custom scripts. - -Copyright (C) 2020 Felipe Marques de Almeida (almeidafmarques@gmail.com) -License: Public Domain - -usage: - falmeida-py [ -h|--help ] [ -v|--version ] [ --license ] - falmeida-py [ -h|--help ] [ ... ] - -options: - -h --help Show this screen - -v --version Show version information - --license Show LEGAL LICENSE information - -commands: - tsv2markdown Command for rapid convertion of tsv or csv to markdown tables. - splitgbk Command to split multisequence genbank files into individual files. - align2subsetgbk Command to subset genbank files based on alignments to a FASTA file. - gbk2fasta Command to convert genbank files to fasta files. - blasts Command to execute automatized blast commands. - replace_fasta_seq Command to replace strings in a FASTA using defitinitions from a BED file - mpgap2csv Command to summarize main mpgap multiqc assembly statistics into a CSV file - bacannot2json Command to summarize main bacannot annotation results into JSON file - -Use: `falmeida-py -h` to get more help and see examples. +Traceback (most recent call last): + File "/home/falmeida/Documents/GitHub/pythonScripts/falmeida-py-runner.py", line 18, in + from falmeida_py.__main__ import main + File "/home/falmeida/Documents/GitHub/pythonScripts/falmeida_py/__main__.py", line 47, in + from docopt import docopt +ModuleNotFoundError: No module named 'docopt' From 86d754757d7f3a1cf08306f9a50ecd5edb3bff51 Mon Sep 17 00:00:00 2001 From: fmalmeida Date: Mon, 27 Feb 2023 19:36:39 +0100 Subject: [PATCH 08/32] update python package --- conda.recipe/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conda.recipe/meta.yaml b/conda.recipe/meta.yaml index b16d576..4bbd0bc 100644 --- a/conda.recipe/meta.yaml +++ b/conda.recipe/meta.yaml @@ -14,7 +14,7 @@ build: requirements: build: - - python >=3.7,{{PY_VER}}* + - python >=3.10,{{PY_VER}}* - setuptools - setuptools-git - pandas From 9931b4201b7c3e87fef07fcb75c41cebcb2c9c33 Mon Sep 17 00:00:00 2001 From: fmalmeida Date: Tue, 28 Feb 2023 11:24:52 +0100 Subject: [PATCH 09/32] fix indentation --- falmeida_py/mges_function.py | 75 +++++++++++++++++------------------- 1 file changed, 36 insertions(+), 39 deletions(-) diff --git a/falmeida_py/mges_function.py b/falmeida_py/mges_function.py index 29d1c46..035355c 100644 --- a/falmeida_py/mges_function.py +++ b/falmeida_py/mges_function.py @@ -17,43 +17,40 @@ def mges_stats(bacannot_summary): # init MGE annotation dictionary bacannot_summary[sample]['MGE'] = {} - - # load annotation stats - if os.path.exists(f"{results_dir}/integron_finder"): - # integron_finder - if os.path.exists(f"{results_dir}/integron_finder/{sample}_integrons.gff"): - - # init integron_finder annotation dictionary - bacannot_summary[sample]['MGE']['integron_finder'] = {} - - # load integron_finder results - results = pd.read_csv( - f"{results_dir}/integron_finder/{sample}_integrons.gff", - sep='\t', - header=None, - names=[ - 'chr', 'source', 'type', 'start', 'end', 'score', 'strand', 'frame', 'atts' - ] - ) - - # number of integron_finder annotations - total_number = len(results.index) - bacannot_summary[sample]['MGE']['integron_finder']['total'] = total_number - - # per integron info - bacannot_summary[sample]['MGE']['integron_finder'] = {} - if int(results.shape[0]) > 0: - for seq in [ str(x) for x in results['chr'].unique() ]: - - bacannot_summary[sample]['MGE']['integron_finder'][seq] = {} - for index, row in results[results['chr'] == seq].reset_index().iterrows(): - id = row['atts'].split(';')[0].split('=')[-1] - bacannot_summary[sample]['MGE']['integron_finder'][seq][id] = {} - bacannot_summary[sample]['MGE']['integron_finder'][seq][id]['id'] = id - bacannot_summary[sample]['MGE']['integron_finder'][seq][id]['contig'] = row['chr'] - bacannot_summary[sample]['MGE']['integron_finder'][seq][id]['start'] = row['start'] - bacannot_summary[sample]['MGE']['integron_finder'][seq][id]['end'] = row['end'] - bacannot_summary[sample]['MGE']['integron_finder'][seq][id]['type'] = row['atts'].split(';')[1].split('=')[-1] - bacannot_summary[sample]['MGE']['integron_finder'][seq][id]['source'] = row['source'] - bacannot_summary[sample]['MGE']['integron_finder'][seq][id]['product'] = row['type'] \ No newline at end of file + # integron_finder + if os.path.exists(f"{results_dir}/integron_finder/{sample}_integrons.gff"): + + # init integron_finder annotation dictionary + bacannot_summary[sample]['MGE']['integron_finder'] = {} + + # load integron_finder results + results = pd.read_csv( + f"{results_dir}/integron_finder/{sample}_integrons.gff", + sep='\t', + header=None, + names=[ + 'chr', 'source', 'type', 'start', 'end', 'score', 'strand', 'frame', 'atts' + ] + ) + + # number of integron_finder annotations + total_number = len(results.index) + bacannot_summary[sample]['MGE']['integron_finder']['total'] = total_number + + # per integron info + bacannot_summary[sample]['MGE']['integron_finder'] = {} + if int(results.shape[0]) > 0: + for seq in [ str(x) for x in results['chr'].unique() ]: + + bacannot_summary[sample]['MGE']['integron_finder'][seq] = {} + for index, row in results[results['chr'] == seq].reset_index().iterrows(): + id = row['atts'].split(';')[0].split('=')[-1] + bacannot_summary[sample]['MGE']['integron_finder'][seq][id] = {} + bacannot_summary[sample]['MGE']['integron_finder'][seq][id]['id'] = id + bacannot_summary[sample]['MGE']['integron_finder'][seq][id]['contig'] = row['chr'] + bacannot_summary[sample]['MGE']['integron_finder'][seq][id]['start'] = row['start'] + bacannot_summary[sample]['MGE']['integron_finder'][seq][id]['end'] = row['end'] + bacannot_summary[sample]['MGE']['integron_finder'][seq][id]['type'] = row['atts'].split(';')[1].split('=')[-1] + bacannot_summary[sample]['MGE']['integron_finder'][seq][id]['source'] = row['source'] + bacannot_summary[sample]['MGE']['integron_finder'][seq][id]['product'] = row['type'] \ No newline at end of file From 713dd3f5eda6349e4268ace752b794c646130ee5 Mon Sep 17 00:00:00 2001 From: fmalmeida Date: Sun, 26 Mar 2023 10:21:44 +0200 Subject: [PATCH 10/32] include mob_suite results parsing to summary --- bacannot_summary.json | 11492 ------------------------------ conda.recipe/meta.yaml | 2 +- falmeida_py/plasmid_function.py | 171 +- falmeida_py/version.py | 2 +- 4 files changed, 110 insertions(+), 11557 deletions(-) delete mode 100644 bacannot_summary.json diff --git a/bacannot_summary.json b/bacannot_summary.json deleted file mode 100644 index 43bc050..0000000 --- a/bacannot_summary.json +++ /dev/null @@ -1,11492 +0,0 @@ -{ - "ecoli_1": { - "MGE": {}, - "general_annotation": { - "cds": 4681, - "closest_reference": { - "accession": "NZ_JTDT", - "distance": 0.00274861, - "strain": "Escherichia coli" - }, - "mlst": "73", - "rrna": 4, - "tmrna": 1, - "trna": 70 - }, - "plasmid": { - "plasmidfinder": {}, - "platon": { - "84": { - "AMRs": 0, - "Circular": "no", - "Conjugation": 0, - "Length": 10558, - "Mobilization": 0, - "ORFs": 5, - "Replication": 0 - } - } - }, - "resistance": { - "amrfinderplus": { - "GOMEMAFE_00009": { - "card_aro": 3000502, - "contig": 1, - "end": 8462, - "gene": "acrF", - "identity": 99.42, - "start": 5358, - "subclass": "EFFLUX", - "type": "AMR" - }, - "GOMEMAFE_00892": { - "card_aro": null, - "contig": 6, - "end": 72884, - "gene": "fieF", - "identity": 99.67, - "start": 71982, - "subclass": null, - "type": "STRESS" - }, - "GOMEMAFE_01968": { - "card_aro": null, - "contig": 17, - "end": 8615, - "gene": "ymgB", - "identity": 97.73, - "start": 8349, - "subclass": null, - "type": "STRESS" - }, - "GOMEMAFE_02188": { - "card_aro": null, - "contig": 20, - "end": 8779, - "gene": "asr", - "identity": 98.04, - "start": 8471, - "subclass": null, - "type": "STRESS" - }, - "GOMEMAFE_02315": { - "card_aro": null, - "contig": 21, - "end": 64895, - "gene": "emrD", - "identity": 99.49, - "start": 63711, - "subclass": "EFFLUX", - "type": "AMR" - }, - "GOMEMAFE_02346": { - "card_aro": 3004039, - "contig": 22, - "end": 15190, - "gene": "emrE", - "identity": 98.18, - "start": 14858, - "subclass": "EFFLUX", - "type": "STRESS" - }, - "GOMEMAFE_02841": { - "card_aro": 3006880, - "contig": 28, - "end": 57085, - "gene": "blaEC-5", - "identity": 100.0, - "start": 55952, - "subclass": "CEPHALOSPORIN", - "type": "AMR" - }, - "GOMEMAFE_03475": { - "card_aro": null, - "contig": 40, - "end": 27348, - "gene": "arsC", - "identity": 93.62, - "start": 26923, - "subclass": "ARSENATE", - "type": "STRESS" - }, - "total": 8 - }, - "resfinder": { - "total": 0 - }, - "rgi": { - "GOMEMAFE_00009": { - "accession": 1437, - "card_aro": 3000502, - "contig": 1, - "cut_off": "Strict", - "end": 8462, - "gene": "AcrF", - "gene_family": "resistance-nodulation-cell division (RND) antibiotic efflux pump", - "identity": 99.42, - "name": "Multidrug export protein AcrF", - "resistance_mechanism": "antibiotic efflux", - "start": 5358, - "subclass": "fluoroquinolone antibiotic; cephalosporin; cephamycin; penam" - }, - "GOMEMAFE_00010": { - "accession": 1445, - "card_aro": 3000499, - "contig": 1, - "cut_off": "Strict", - "end": 9631, - "gene": "AcrE", - "gene_family": "resistance-nodulation-cell division (RND) antibiotic efflux pump", - "identity": 99.48, - "name": "Multidrug export protein AcrE", - "resistance_mechanism": "antibiotic efflux", - "start": 8474, - "subclass": "fluoroquinolone antibiotic; cephalosporin; cephamycin; penam" - }, - "GOMEMAFE_00011": { - "accession": 520, - "card_aro": 3000656, - "contig": 1, - "cut_off": "Strict", - "end": 10692, - "gene": "AcrS", - "gene_family": "resistance-nodulation-cell division (RND) antibiotic efflux pump", - "identity": 98.18, - "name": "HTH-type transcriptional regulator AcrR", - "resistance_mechanism": "antibiotic efflux", - "start": 10030, - "subclass": "fluoroquinolone antibiotic; cephalosporin; glycylcycline; cephamycin; penam; tetracycline antibiotic; rifamycin antibiotic; phenicol antibiotic; disinfecting agents and antiseptics" - }, - "GOMEMAFE_00231": { - "accession": 1427, - "card_aro": 3000491, - "contig": 2, - "cut_off": "Strict", - "end": 47007, - "gene": "acrD", - "gene_family": "resistance-nodulation-cell division (RND) antibiotic efflux pump", - "identity": 99.71, - "name": "Multidrug efflux pump subunit AcrB", - "resistance_mechanism": "antibiotic efflux", - "start": 43894, - "subclass": "aminoglycoside antibiotic" - }, - "GOMEMAFE_00318": { - "accession": 1318, - "card_aro": 3000833, - "contig": 2, - "cut_off": "Strict", - "end": 138605, - "gene": "evgS", - "gene_family": "major facilitator superfamily (MFS) antibiotic efflux pump; resistance-nodulation-cell division (RND) antibiotic efflux pump", - "identity": 96.66, - "name": "Sensor protein EvgS", - "resistance_mechanism": "antibiotic efflux", - "start": 135012, - "subclass": "macrolide antibiotic; fluoroquinolone antibiotic; penam; tetracycline antibiotic" - }, - "GOMEMAFE_00319": { - "accession": 1015, - "card_aro": 3000832, - "contig": 2, - "cut_off": "Perfect", - "end": 139224, - "gene": "evgA", - "gene_family": "major facilitator superfamily (MFS) antibiotic efflux pump; resistance-nodulation-cell division (RND) antibiotic efflux pump", - "identity": 100.0, - "name": "DNA-binding transcriptional activator EvgA", - "resistance_mechanism": "antibiotic efflux", - "start": 138610, - "subclass": "macrolide antibiotic; fluoroquinolone antibiotic; penam; tetracycline antibiotic" - }, - "GOMEMAFE_00320": { - "accession": 609, - "card_aro": 3000206, - "contig": 2, - "cut_off": "Strict", - "end": 140803, - "gene": "emrK", - "gene_family": "major facilitator superfamily (MFS) antibiotic efflux pump", - "identity": 98.86, - "name": "putative multidrug resistance protein EmrK", - "resistance_mechanism": "antibiotic efflux", - "start": 139640, - "subclass": "tetracycline antibiotic" - }, - "GOMEMAFE_00321": { - "accession": 540, - "card_aro": 3000254, - "contig": 2, - "cut_off": "Strict", - "end": 142341, - "gene": "emrY", - "gene_family": "major facilitator superfamily (MFS) antibiotic efflux pump", - "identity": 99.8, - "name": "putative multidrug resistance protein EmrY", - "resistance_mechanism": "antibiotic efflux", - "start": 140803, - "subclass": "tetracycline antibiotic" - }, - "GOMEMAFE_00431": { - "accession": 1330, - "card_aro": 3000516, - "contig": 3, - "cut_off": "Perfect", - "end": 51266, - "gene": "emrR", - "gene_family": "major facilitator superfamily (MFS) antibiotic efflux pump", - "identity": 100.0, - "name": "Transcriptional repressor MprA", - "resistance_mechanism": "antibiotic efflux", - "start": 50736, - "subclass": "fluoroquinolone antibiotic" - }, - "GOMEMAFE_00432": { - "accession": 1757, - "card_aro": 3000027, - "contig": 3, - "cut_off": "Strict", - "end": 52565, - "gene": "emrA", - "gene_family": "major facilitator superfamily (MFS) antibiotic efflux pump", - "identity": 99.74, - "name": "Multidrug export protein EmrA", - "resistance_mechanism": "antibiotic efflux", - "start": 51393, - "subclass": "fluoroquinolone antibiotic" - }, - "GOMEMAFE_00433": { - "accession": 1847, - "card_aro": 3000074, - "contig": 3, - "cut_off": "Strict", - "end": 54120, - "gene": "emrB", - "gene_family": "major facilitator superfamily (MFS) antibiotic efflux pump", - "identity": 99.8, - "name": "Multidrug export protein EmrB", - "resistance_mechanism": "antibiotic efflux", - "start": 52582, - "subclass": "fluoroquinolone antibiotic" - }, - "GOMEMAFE_00739": { - "accession": 2424, - "card_aro": 3003952, - "contig": 5, - "cut_off": "Strict", - "end": 24184, - "gene": "YojI", - "gene_family": "ATP-binding cassette (ABC) antibiotic efflux pump", - "identity": 99.63, - "name": "ABC transporter ATP-binding/permease protein YojI", - "resistance_mechanism": "antibiotic efflux", - "start": 22541, - "subclass": "peptide antibiotic" - }, - "GOMEMAFE_00766": { - "accession": 2372, - "card_aro": 3003889, - "contig": 5, - "cut_off": "Strict", - "end": 66818, - "gene": "Escherichia coli GlpT with mutation conferring resistance to fosfomycin", - "gene_family": "antibiotic-resistant GlpT", - "identity": 99.52, - "name": "Glycerol-3-phosphate transporter", - "resistance_mechanism": "antibiotic target alteration", - "start": 66195, - "subclass": "phosphonic acid antibiotic" - }, - "GOMEMAFE_00781": { - "accession": 2014, - "card_aro": 3003578, - "contig": 5, - "cut_off": "Strict", - "end": 83047, - "gene": "PmrF", - "gene_family": "pmr phosphoethanolamine transferase", - "identity": 99.38, - "name": "Undecaprenyl-phosphate 4-deoxy-4-formamido-L-arabinose transferase", - "resistance_mechanism": "antibiotic target alteration", - "start": 82079, - "subclass": "peptide antibiotic" - }, - "GOMEMAFE_00895": { - "accession": 152, - "card_aro": 3000830, - "contig": 6, - "cut_off": "Perfect", - "end": 75751, - "gene": "cpxA", - "gene_family": "resistance-nodulation-cell division (RND) antibiotic efflux pump", - "identity": 100.0, - "name": "Sensor histidine kinase CpxA", - "resistance_mechanism": "antibiotic efflux", - "start": 74378, - "subclass": "aminoglycoside antibiotic; aminocoumarin antibiotic" - }, - "GOMEMAFE_01051": { - "accession": 826, - "card_aro": 3000237, - "contig": 7, - "cut_off": "Strict", - "end": 107908, - "gene": "TolC", - "gene_family": "ATP-binding cassette (ABC) antibiotic efflux pump; major facilitator superfamily (MFS) antibiotic efflux pump; resistance-nodulation-cell division (RND) antibiotic efflux pump", - "identity": 99.59, - "name": "Outer membrane protein TolC", - "resistance_mechanism": "antibiotic efflux", - "start": 106427, - "subclass": "macrolide antibiotic; fluoroquinolone antibiotic; aminoglycoside antibiotic; carbapenem; cephalosporin; glycylcycline; cephamycin; penam; tetracycline antibiotic; peptide antibiotic; aminocoumarin antibiotic; rifamycin antibiotic; phenicol antibiotic; penem; disinfecting agents and antiseptics" - }, - "GOMEMAFE_01431": { - "accession": 2423, - "card_aro": 3003950, - "contig": 11, - "cut_off": "Strict", - "end": 51647, - "gene": "msbA", - "gene_family": "ATP-binding cassette (ABC) antibiotic efflux pump", - "identity": 99.66, - "name": "Lipid A export ATP-binding/permease protein MsbA", - "resistance_mechanism": "antibiotic efflux", - "start": 49899, - "subclass": "nitroimidazole antibiotic" - }, - "GOMEMAFE_01545": { - "accession": 37, - "card_aro": 3001328, - "contig": 12, - "cut_off": "Strict", - "end": 57024, - "gene": "Escherichia coli mdfA", - "gene_family": "major facilitator superfamily (MFS) antibiotic efflux pump", - "identity": 97.07, - "name": "Multidrug transporter MdfA", - "resistance_mechanism": "antibiotic efflux", - "start": 55792, - "subclass": "tetracycline antibiotic; disinfecting agents and antiseptics" - }, - "GOMEMAFE_01662": { - "accession": 2066, - "card_aro": 3003511, - "contig": 13, - "cut_off": "Strict", - "end": 85591, - "gene": "Escherichia coli soxS with mutation conferring antibiotic resistance", - "gene_family": "ATP-binding cassette (ABC) antibiotic efflux pump; major facilitator superfamily (MFS) antibiotic efflux pump; resistance-nodulation-cell division (RND) antibiotic efflux pump; General Bacterial Porin with reduced permeability to beta-lactams", - "identity": 100.0, - "name": "Regulatory protein SoxS", - "resistance_mechanism": "antibiotic target alteration; antibiotic efflux; reduced permeability to antibiotic", - "start": 85268, - "subclass": "fluoroquinolone antibiotic; monobactam; carbapenem; cephalosporin; glycylcycline; cephamycin; penam; tetracycline antibiotic; rifamycin antibiotic; phenicol antibiotic; penem; disinfecting agents and antiseptics" - }, - "GOMEMAFE_01663": { - "accession": 1005, - "card_aro": 3003381, - "contig": 13, - "cut_off": "Strict", - "end": 86141, - "gene": "Escherichia coli soxR with mutation conferring antibiotic resistance", - "gene_family": "ATP-binding cassette (ABC) antibiotic efflux pump; major facilitator superfamily (MFS) antibiotic efflux pump; resistance-nodulation-cell division (RND) antibiotic efflux pump", - "identity": 99.35, - "name": "Redox-sensitive transcriptional activator SoxR", - "resistance_mechanism": "antibiotic target alteration; antibiotic efflux", - "start": 85677, - "subclass": "fluoroquinolone antibiotic; cephalosporin; glycylcycline; penam; tetracycline antibiotic; rifamycin antibiotic; phenicol antibiotic; disinfecting agents and antiseptics" - }, - "GOMEMAFE_01771": { - "accession": 2331, - "card_aro": 3003841, - "contig": 14, - "cut_off": "Strict", - "end": 92341, - "gene": "kdpE", - "gene_family": "kdpDE", - "identity": 99.55, - "name": "KDP operon transcriptional regulatory protein KdpE", - "resistance_mechanism": "antibiotic efflux", - "start": 91664, - "subclass": "aminoglycoside antibiotic" - }, - "GOMEMAFE_01889": { - "accession": 869, - "card_aro": 3000518, - "contig": 16, - "cut_off": "Strict", - "end": 15657, - "gene": "CRP", - "gene_family": "resistance-nodulation-cell division (RND) antibiotic efflux pump", - "identity": 99.52, - "name": "cAMP-activated global transcriptional regulator CRP", - "resistance_mechanism": "antibiotic efflux", - "start": 15025, - "subclass": "macrolide antibiotic; fluoroquinolone antibiotic; penam" - }, - "GOMEMAFE_02050": { - "accession": 1248, - "card_aro": 3000676, - "contig": 17, - "cut_off": "Perfect", - "end": 90083, - "gene": "H-NS", - "gene_family": "major facilitator superfamily (MFS) antibiotic efflux pump; resistance-nodulation-cell division (RND) antibiotic efflux pump", - "identity": 100.0, - "name": "DNA-binding protein H-NS", - "resistance_mechanism": "antibiotic efflux", - "start": 89670, - "subclass": "macrolide antibiotic; fluoroquinolone antibiotic; cephalosporin; cephamycin; penam; tetracycline antibiotic" - }, - "GOMEMAFE_02223": { - "accession": 1922, - "card_aro": 3000263, - "contig": 20, - "cut_off": "Strict", - "end": 45371, - "gene": "marA", - "gene_family": "resistance-nodulation-cell division (RND) antibiotic efflux pump; General Bacterial Porin with reduced permeability to beta-lactams", - "identity": 99.21, - "name": "Multiple antibiotic resistance protein MarA", - "resistance_mechanism": "antibiotic efflux; reduced permeability to antibiotic", - "start": 44988, - "subclass": "fluoroquinolone antibiotic; monobactam; carbapenem; cephalosporin; glycylcycline; cephamycin; penam; tetracycline antibiotic; rifamycin antibiotic; phenicol antibiotic; penem; disinfecting agents and antiseptics" - }, - "GOMEMAFE_02224": { - "accession": 431, - "card_aro": 3003378, - "contig": 20, - "cut_off": "Strict", - "end": 45826, - "gene": "Escherichia coli AcrAB-TolC with MarR mutations conferring resistance to ciprofloxacin and tetracycline", - "gene_family": "resistance-nodulation-cell division (RND) antibiotic efflux pump", - "identity": 98.61, - "name": "Multiple antibiotic resistance protein MarR", - "resistance_mechanism": "antibiotic target alteration; antibiotic efflux", - "start": 45392, - "subclass": "fluoroquinolone antibiotic; cephalosporin; glycylcycline; penam; tetracycline antibiotic; rifamycin antibiotic; phenicol antibiotic; disinfecting agents and antiseptics" - 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"end": 3248764, - "id": "24112632", - "name": "UTP-glucose-1-phosphate_uridylyltransferase", - "product": "gi|24112632|ref|NP_707142.1|UTP-glucose-1-phosphate_uridylyltransferase_[Shigella_flexneri_2a_str._301]", - "start": 3247862 - }, - "FKEDNGPL_03173": { - "contig": "NZ_CP006659.2", - "end": 3296054, - "id": "117623421", - "name": "GTP-dependent_nucleic_acid-binding_protein_EngD", - "product": "gi|117623421|ref|YP_852334.1|GTP-dependent_nucleic_acid-binding_protein_EngD_[Escherichia_coli_APEC_O1]", - "start": 3294963 - }, - "FKEDNGPL_03251": { - "contig": "NZ_CP006659.2", - "end": 3379910, - "id": "16765159", - "name": "long-chain-fatty-acid--CoA_ligase", - "product": "gi|16765159|ref|NP_460774.1|long-chain-fatty-acid--CoA_ligase_[Salmonella_enterica_subsp._enterica_serovar_Typhimurium_str._LT2]", - "start": 3378192 - }, - "FKEDNGPL_03269": { - "contig": "NZ_CP006659.2", - "end": 3398678, - "id": "15802236", - "name": "cold_shock-like_protein_CspC", - "product": "gi|15802236|ref|NP_288259.1|cold_shock-like_protein_CspC_[Escherichia_coli_O157:H7_str._EDL933]", - "start": 3398469 - }, - "FKEDNGPL_03303": { - "contig": "NZ_CP006659.2", - "end": 3434751, - "id": "39546331", - "name": "zinc_ABC_transporter_ATP-binding_protein_ZnuC", - "product": "gi|39546331|ref|NP_460849.2|zinc_ABC_transporter_ATP-binding_protein_ZnuC_[Salmonella_enterica_subsp._enterica_serovar_Typhimurium_str._LT2]", - "start": 3433999 - }, - "FKEDNGPL_03304": { - "contig": "NZ_CP006659.2", - "end": 3435536, - "id": "16765235", - "name": "zinc_ABC_transporter_permease_ZnuB", - "product": "gi|16765235|ref|NP_460850.1|zinc_ABC_transporter_permease_ZnuB_[Salmonella_enterica_subsp._enterica_serovar_Typhimurium_str._LT2]", - "start": 3434751 - }, - "FKEDNGPL_03342": { - "contig": "NZ_CP006659.2", - "end": 3471454, - "id": "16765285", - "name": "LuxR/UhpA_family_response_regulator", - "product": "gi|16765285|ref|NP_460900.1|LuxR/UhpA_family_response_regulator_[Salmonella_enterica_subsp._enterica_serovar_Typhimurium_str._LT2]", - "start": 3470798 - }, - "FKEDNGPL_03445": { - "contig": "NZ_CP006659.2", - "end": 3579164, - "id": "16765428", - "name": "UTP--glucose-1-phosphate_uridylyltransferase_subunit_GalF", - "product": "gi|16765428|ref|NP_461043.1|UTP--glucose-1-phosphate_uridylyltransferase_subunit_GalF_[Salmonella_enterica_subsp._enterica_serovar_Typhimurium_str._LT2]", - "start": 3578316 - }, - "FKEDNGPL_03499": { - "contig": "NZ_CP006659.2", - "end": 3636422, - "id": "16765465", - "name": "protease", - "product": "gi|16765465|ref|NP_461080.1|protease_[Salmonella_enterica_subsp._enterica_serovar_Typhimurium_str._LT2]", - "start": 3635061 - }, - "FKEDNGPL_03686": { - "contig": "NZ_CP006659.2", - "end": 3850710, - "id": "16761308", - "name": "chorismate_synthase", - "product": "gi|16761308|ref|NP_456925.1|chorismate_synthase_[Salmonella_enterica_subsp._enterica_serovar_Typhi_str._CT18]", - "start": 3849625 - }, - "FKEDNGPL_03792": { - "contig": "NZ_CP006659.2", - "end": 3959792, - "id": "16765821", - "name": "polyphosphate_kinase", - "product": "gi|16765821|ref|NP_461436.1|polyphosphate_kinase_[Salmonella_enterica_subsp._enterica_serovar_Typhimurium_str._LT2]", - "start": 3957732 - }, - "FKEDNGPL_03853": { - "contig": "NZ_CP006659.2", - "end": 4011931, - "id": "24113836", - "name": "GMP_synthase", - "product": "gi|24113836|ref|NP_708346.1|GMP_synthase_[Shigella_flexneri_2a_str._301]", - "start": 4010354 - }, - "FKEDNGPL_03854": { - "contig": "NZ_CP006659.2", - "end": 4013465, - "id": "56480121", - "name": "inosine_5'-monophosphate_dehydrogenase", - "product": "gi|56480121|ref|NP_708347.2|inosine_5'-monophosphate_dehydrogenase_[Shigella_flexneri_2a_str._301]", - "start": 4011999 - }, - "FKEDNGPL_03903": { - "contig": "NZ_CP006659.2", - "end": 4073409, - "id": "16765896", - "name": "ferredoxin", - "product": "gi|16765896|ref|NP_461511.1|ferredoxin_[Salmonella_enterica_subsp._enterica_serovar_Typhimurium_str._LT2]", - "start": 4073149 - }, - "FKEDNGPL_03932": { - "contig": "NZ_CP006659.2", - "end": 4105356, - "id": "16765976", - "name": "chaperone_protein_ClpB", - "product": "gi|16765976|ref|NP_461591.1|chaperone_protein_ClpB_[Salmonella_enterica_subsp._enterica_serovar_Typhimurium_str._LT2]", - "start": 4102783 - }, - "FKEDNGPL_04406": { - "contig": "NZ_CP006659.2", - "end": 4580961, - "id": "15803477", - "name": "arginine_decarboxylase", - "product": "gi|15803477|ref|NP_289510.1|arginine_decarboxylase_[Escherichia_coli_O157:H7_str._EDL933]", - "start": 4578985 - }, - "FKEDNGPL_04717": { - "contig": "NZ_CP006659.2", - "end": 4884708, - "id": "16766637", - "name": "stringent_starvation_protein_A", - "product": "gi|16766637|ref|NP_462252.1|stringent_starvation_protein_A_[Salmonella_enterica_subsp._enterica_serovar_Typhimurium_str._LT2]", - "start": 4884070 - }, - "FKEDNGPL_04846": { - "contig": "NZ_CP006659.2", - "end": 4989716, - "id": "16766754", - "name": "cAMP-activated_global_transcriptional_regulator", - "product": "gi|16766754|ref|NP_462369.1|cAMP-activated_global_transcriptional_regulator_[Salmonella_enterica_subsp._enterica_serovar_Typhimurium_str._LT2]", - "start": 4989084 - }, - "FKEDNGPL_04877": { - "contig": "NZ_CP006659.2", - "end": 5023818, - "id": "16766789", - "name": "osmolarity_sensor_protein_EnvZ", - "product": "gi|16766789|ref|NP_462404.1|osmolarity_sensor_protein_EnvZ_[Salmonella_enterica_subsp._enterica_serovar_Typhimurium_str._LT2]", - "start": 5022463 - }, - "FKEDNGPL_04878": { - "contig": "NZ_CP006659.2", - "end": 5024534, - "id": "56480330", - "name": "osmolarity_response_regulator", - "product": "gi|56480330|ref|NP_709178.2|osmolarity_response_regulator_[Shigella_flexneri_2a_str._301]", - "start": 5023815 - }, - "FKEDNGPL_05003": { - "contig": "NZ_CP006659.2", - "end": 5176986, - "id": "117625828", - "name": "dipeptide_transporter_protein_DppA", - "product": "gi|117625828|ref|YP_859151.1|dipeptide_transporter_protein_DppA_[Escherichia_coli_APEC_O1]", - "start": 5175379 - }, - "FKEDNGPL_05102": { - "contig": "NZ_CP006659.2", - "end": 5282416, - "id": "22124023", - "name": "bifunctional_(p)ppGpp_synthetase_II/_guanosine-3',5'-bis_pyrophosphate_3'-pyrophosphohydrolase", - "product": "gi|22124023|ref|NP_667446.1|bifunctional_(p)ppGpp_synthetase_II/_guanosine-3',5'-bis_pyrophosphate_3'-pyrophosphohydrolase_[Yersinia_pestis_KIM10+]", - "start": 5280296 - }, - "FKEDNGPL_05198": { - "contig": "NZ_CP006659.2", - "end": 5381601, - "id": "228960701", - "name": "heat_shock_protein_IbpA", - "product": "gi|228960701|ref|NP_462709.3|heat_shock_protein_IbpA_[Salmonella_enterica_subsp._enterica_serovar_Typhimurium_str._LT2]", - "start": 5381188 - }, - "total": 53 - } - } - } -} \ No newline at end of file diff --git a/conda.recipe/meta.yaml b/conda.recipe/meta.yaml index 4bbd0bc..889c95e 100644 --- a/conda.recipe/meta.yaml +++ b/conda.recipe/meta.yaml @@ -1,6 +1,6 @@ package: name: falmeida-py - version: '1.1.0' + version: '1.2.0' source: path: .. diff --git a/falmeida_py/plasmid_function.py b/falmeida_py/plasmid_function.py index 86e00a8..8cd6a66 100644 --- a/falmeida_py/plasmid_function.py +++ b/falmeida_py/plasmid_function.py @@ -15,72 +15,117 @@ def plasmids_stats(bacannot_summary): # load dir of samples' results results_dir = bacannot_summary[sample]['results_dir'] - # load annotation stats - if os.path.exists(f"{results_dir}/plasmids"): - - # init plasmids annotation dictionary - bacannot_summary[sample]['plasmid'] = {} + # init plasmids annotation dictionary + bacannot_summary[sample]['plasmid'] = {} - # platon - if os.path.exists(f"{results_dir}/plasmids/platon/{sample}.tsv"): + # platon + if os.path.exists(f"{results_dir}/plasmids/platon/{sample}.tsv"): + + # init platon annotation dictionary + bacannot_summary[sample]['plasmid']['platon'] = {} + + # load platon results + results = pd.read_csv( + f"{results_dir}/plasmids/platon/{sample}.tsv", + sep='\t' + ) + + # number of plasmid annotations + total_number = len(results.index) + bacannot_summary[sample]['plasmid']['platon']['total'] = total_number + + # per plasmid info + if int(results.shape[0]) > 0: + for seq in [x for x in results['ID'].unique()]: + bacannot_summary[sample]['plasmid']['platon'][seq] = {} + bacannot_summary[sample]['plasmid']['platon'][seq]['Length'] = results.loc[results['ID'] == seq, 'Length'].item() + bacannot_summary[sample]['plasmid']['platon'][seq]['ORFs'] = results.loc[results['ID'] == seq, '# ORFs'].item() + bacannot_summary[sample]['plasmid']['platon'][seq]['Circular'] = results.loc[results['ID'] == seq, 'Circular'].item() + bacannot_summary[sample]['plasmid']['platon'][seq]['AMRs'] = results.loc[results['ID'] == seq, '# AMRs'].item() + bacannot_summary[sample]['plasmid']['platon'][seq]['Replication'] = results.loc[results['ID'] == seq, '# Replication'].item() + bacannot_summary[sample]['plasmid']['platon'][seq]['Mobilization'] = results.loc[results['ID'] == seq, '# Mobilization'].item() + bacannot_summary[sample]['plasmid']['platon'][seq]['Conjugation'] = results.loc[results['ID'] == seq, '# Conjugation'].item() + + # plasmidfinder + if os.path.exists(f"{results_dir}/plasmids/plasmidfinder/results_tab.tsv"): + + # init platon annotation dictionary + bacannot_summary[sample]['plasmid']['plasmidfinder'] = {} + + # load platon results + results = pd.read_csv( + f"{results_dir}/plasmids/plasmidfinder/results_tab.tsv", + sep='\t' + ) - # init platon annotation dictionary - bacannot_summary[sample]['plasmid']['platon'] = {} + if not results.empty: - # load platon results - results = pd.read_csv( - f"{results_dir}/plasmids/platon/{sample}.tsv", - sep='\t' - ) + # databases + bacannot_summary[sample]['plasmid']['plasmidfinder']['meta'] = {} + bacannot_summary[sample]['plasmid']['plasmidfinder']['meta']['database'] = results['Database'].unique().item() # number of plasmid annotations - total_number = len(results.index) - bacannot_summary[sample]['plasmid']['platon']['total'] = total_number - - # per plasmid info - bacannot_summary[sample]['plasmid']['platon'] = {} - if int(results.shape[0]) > 0: - for seq in [x for x in results['ID'].unique()]: - bacannot_summary[sample]['plasmid']['platon'][seq] = {} - bacannot_summary[sample]['plasmid']['platon'][seq]['Length'] = results.loc[results['ID'] == seq, 'Length'].item() - bacannot_summary[sample]['plasmid']['platon'][seq]['ORFs'] = results.loc[results['ID'] == seq, '# ORFs'].item() - bacannot_summary[sample]['plasmid']['platon'][seq]['Circular'] = results.loc[results['ID'] == seq, 'Circular'].item() - bacannot_summary[sample]['plasmid']['platon'][seq]['AMRs'] = results.loc[results['ID'] == seq, '# AMRs'].item() - bacannot_summary[sample]['plasmid']['platon'][seq]['Replication'] = results.loc[results['ID'] == seq, '# Replication'].item() - bacannot_summary[sample]['plasmid']['platon'][seq]['Mobilization'] = results.loc[results['ID'] == seq, '# Mobilization'].item() - bacannot_summary[sample]['plasmid']['platon'][seq]['Conjugation'] = results.loc[results['ID'] == seq, '# Conjugation'].item() - - # plasmidfinder - if os.path.exists(f"{results_dir}/plasmids/plasmidfinder/results_tab.tsv"): - - # init platon annotation dictionary - bacannot_summary[sample]['plasmid']['plasmidfinder'] = {} - - # load platon results - results = pd.read_csv( - f"{results_dir}/plasmids/plasmidfinder/results_tab.tsv", - sep='\t' - ) - - if not results.empty: - - # databases - bacannot_summary[sample]['plasmid']['plasmidfinder']['meta'] = {} - bacannot_summary[sample]['plasmid']['plasmidfinder']['meta']['database'] = results['Database'].unique().item() - - # number of plasmid annotations - total_number = len(results['Contig'].unique()) - bacannot_summary[sample]['plasmid']['plasmidfinder']['total'] = total_number - - # plasmid annotations contigs - for seq in [ str(x) for x in results['Contig'].unique() ]: - bacannot_summary[sample]['plasmid']['plasmidfinder'][seq] = {} - bacannot_summary[sample]['plasmid']['plasmidfinder'][seq]['inc_types'] = {} - bacannot_summary[sample]['plasmid']['plasmidfinder'][seq]['identity'] = {} - bacannot_summary[sample]['plasmid']['plasmidfinder'][seq]['accession'] = {} + total_number = len(results['Contig'].unique()) + bacannot_summary[sample]['plasmid']['plasmidfinder']['total'] = total_number + + # plasmid annotations contigs + for seq in [ str(x) for x in results['Contig'].unique() ]: + bacannot_summary[sample]['plasmid']['plasmidfinder'][seq] = {} + bacannot_summary[sample]['plasmid']['plasmidfinder'][seq]['inc_types'] = {} + bacannot_summary[sample]['plasmid']['plasmidfinder'][seq]['identity'] = {} + bacannot_summary[sample]['plasmid']['plasmidfinder'][seq]['accession'] = {} + + for index, row in results.iterrows(): + contig = str(row['Contig']) + bacannot_summary[sample]['plasmid']['plasmidfinder'][contig]['inc_types'] = row['Plasmid'] + bacannot_summary[sample]['plasmid']['plasmidfinder'][contig]['identity'] = row['Identity'] + bacannot_summary[sample]['plasmid']['plasmidfinder'][contig]['accession'] = row['Accession number'] + + # mob suite + if os.path.exists(f"{results_dir}/mob_suite/{sample}_mobtyper_results.txt"): + + # init integron_finder annotation dictionary + bacannot_summary[sample]['plasmid']['mob_suite'] = {} + + # load integron_finder results + results = pd.read_csv( + f"{results_dir}/mob_suite/{sample}_mobtyper_results.txt", + sep='\t', + header='infer', + # sample_id num_contigs size gc md5 rep_type(s) rep_type_accession(s) relaxase_type(s) relaxase_type_accession(s) mpf_type mpf_type_accession(s) orit_type(s) orit_accession(s) predicted_mobility mash_nearest_neighbor mash_neighbor_distance mash_neighbor_identification primary_cluster_id secondary_cluster_id predicted_host_range_overall_rank predicted_host_range_overall_name observed_host_range_ncbi_rank observed_host_range_ncbi_name reported_host_range_lit_rank reported_host_range_lit_name associated_pmid(s) + ) + + # number of plasmid types annotated annotations + # total_number = len(results.index) - 1 # always counts chromosome + # bacannot_summary[sample]['plasmid']['mob_suite']['total'] = total_number + + # per integron info + bacannot_summary[sample]['plasmid']['mob_suite'] = {} + if int(results.shape[0]) > 0: + for seq in [ str(x) for x in results['sample_id'].unique() ]: - for index, row in results.iterrows(): - contig = str(row['Contig']) - bacannot_summary[sample]['plasmid']['plasmidfinder'][contig]['inc_types'] = row['Plasmid'] - bacannot_summary[sample]['plasmid']['plasmidfinder'][contig]['identity'] = row['Identity'] - bacannot_summary[sample]['plasmid']['plasmidfinder'][contig]['accession'] = row['Accession number'] \ No newline at end of file + bacannot_summary[sample]['plasmid']['mob_suite'][seq] = {} + for index, row in results[results['sample_id'] == seq].reset_index().iterrows(): + id = row['sample_id'] # they are the same for this result + bacannot_summary[sample]['plasmid']['mob_suite'][seq][id] = {} + bacannot_summary[sample]['plasmid']['mob_suite'][seq][id]['size'] = row['size'] + bacannot_summary[sample]['plasmid']['mob_suite'][seq][id]['rep_type'] = row['rep_type(s)'].replace(',', '; ') + bacannot_summary[sample]['plasmid']['mob_suite'][seq][id]['rep_type_accession'] = row['rep_type_accession(s)'].replace(',', '; ') + bacannot_summary[sample]['plasmid']['mob_suite'][seq][id]['relaxase_type'] = row['relaxase_type(s)'] + bacannot_summary[sample]['plasmid']['mob_suite'][seq][id]['relaxase_type_accession(s)'] = row['relaxase_type_accession(s)'] + bacannot_summary[sample]['plasmid']['mob_suite'][seq][id]['mpf_type'] = row['mpf_type'] + bacannot_summary[sample]['plasmid']['mob_suite'][seq][id]['mpf_type_accession'] = row['mpf_type_accession(s)'] + bacannot_summary[sample]['plasmid']['mob_suite'][seq][id]['orit_type'] = row['orit_type(s)'] + bacannot_summary[sample]['plasmid']['mob_suite'][seq][id]['orit_accession'] = row['orit_accession(s)'] + bacannot_summary[sample]['plasmid']['mob_suite'][seq][id]['mash_nearest_neighbor'] = row['mash_nearest_neighbor'] + bacannot_summary[sample]['plasmid']['mob_suite'][seq][id]['mash_neighbor_distance'] = row['mash_neighbor_distance'] + bacannot_summary[sample]['plasmid']['mob_suite'][seq][id]['mash_neighbor_identification'] = row['mash_neighbor_identification'] + bacannot_summary[sample]['plasmid']['mob_suite'][seq][id]['primary_cluster_id'] = row['primary_cluster_id'] + bacannot_summary[sample]['plasmid']['mob_suite'][seq][id]['secondary_cluster_id'] = row['secondary_cluster_id'] + bacannot_summary[sample]['plasmid']['mob_suite'][seq][id]['predicted_host_range_overall_rank'] = row['predicted_host_range_overall_rank'] + bacannot_summary[sample]['plasmid']['mob_suite'][seq][id]['predicted_host_range_overall_name'] = row['predicted_host_range_overall_name'] + bacannot_summary[sample]['plasmid']['mob_suite'][seq][id]['observed_host_range_ncbi_rank'] = row['observed_host_range_ncbi_rank'] + bacannot_summary[sample]['plasmid']['mob_suite'][seq][id]['observed_host_range_ncbi_name'] = row['observed_host_range_ncbi_name'] + bacannot_summary[sample]['plasmid']['mob_suite'][seq][id]['reported_host_range_lit_rank'] = row['reported_host_range_lit_rank'] + bacannot_summary[sample]['plasmid']['mob_suite'][seq][id]['reported_host_range_lit_name'] = row['reported_host_range_lit_name'] + bacannot_summary[sample]['plasmid']['mob_suite'][seq][id]['associated_pmid'] = row['associated_pmid(s)'] \ No newline at end of file diff --git a/falmeida_py/version.py b/falmeida_py/version.py index 73273b3..e1ef2f0 100644 --- a/falmeida_py/version.py +++ b/falmeida_py/version.py @@ -14,7 +14,7 @@ If not, see . """ -__version__ = '1.1.0' +__version__ = '1.2.0' def get_version(): return __version__ From 9abb77a218316edeaed11ca112fca34be13fc910 Mon Sep 17 00:00:00 2001 From: fmalmeida Date: Sun, 26 Mar 2023 15:27:43 +0200 Subject: [PATCH 11/32] Update plasmid_function.py --- falmeida_py/plasmid_function.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/falmeida_py/plasmid_function.py b/falmeida_py/plasmid_function.py index 8cd6a66..20854eb 100644 --- a/falmeida_py/plasmid_function.py +++ b/falmeida_py/plasmid_function.py @@ -82,14 +82,14 @@ def plasmids_stats(bacannot_summary): bacannot_summary[sample]['plasmid']['plasmidfinder'][contig]['accession'] = row['Accession number'] # mob suite - if os.path.exists(f"{results_dir}/mob_suite/{sample}_mobtyper_results.txt"): + if os.path.exists(f"{results_dir}/plasmids/mob_suite/{sample}_mobtyper_results.txt"): # init integron_finder annotation dictionary bacannot_summary[sample]['plasmid']['mob_suite'] = {} # load integron_finder results results = pd.read_csv( - f"{results_dir}/mob_suite/{sample}_mobtyper_results.txt", + f"{results_dir}/plasmids/mob_suite/{sample}_mobtyper_results.txt", sep='\t', header='infer', # sample_id num_contigs size gc md5 rep_type(s) rep_type_accession(s) relaxase_type(s) relaxase_type_accession(s) mpf_type mpf_type_accession(s) orit_type(s) orit_accession(s) predicted_mobility mash_nearest_neighbor mash_neighbor_distance mash_neighbor_identification primary_cluster_id secondary_cluster_id predicted_host_range_overall_rank predicted_host_range_overall_name observed_host_range_ncbi_rank observed_host_range_ncbi_name reported_host_range_lit_rank reported_host_range_lit_name associated_pmid(s) From ea818bc93b1e288d8f10aab227247e0ae971cb21 Mon Sep 17 00:00:00 2001 From: fmalmeida Date: Fri, 5 May 2023 09:02:02 +0200 Subject: [PATCH 12/32] Update meta.yaml --- conda.recipe/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/conda.recipe/meta.yaml b/conda.recipe/meta.yaml index 889c95e..985b5be 100644 --- a/conda.recipe/meta.yaml +++ b/conda.recipe/meta.yaml @@ -14,7 +14,7 @@ build: requirements: build: - - python >=3.10,{{PY_VER}}* + - python>=3.8 - setuptools - setuptools-git - pandas @@ -26,7 +26,7 @@ requirements: - pyyaml run: - - python {{PY_VER}}* + - python>=3.8 - setuptools - setuptools-git - pandas From dc458df014f7ec0ae778eab321995108335bb881 Mon Sep 17 00:00:00 2001 From: fmalmeida Date: Wed, 19 Jul 2023 14:58:01 +0200 Subject: [PATCH 13/32] fix function to understand more than 1 database --- falmeida_py/plasmid_function.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/falmeida_py/plasmid_function.py b/falmeida_py/plasmid_function.py index 20854eb..d7cb62e 100644 --- a/falmeida_py/plasmid_function.py +++ b/falmeida_py/plasmid_function.py @@ -61,8 +61,10 @@ def plasmids_stats(bacannot_summary): if not results.empty: # databases + print( results['Database'].unique() ) bacannot_summary[sample]['plasmid']['plasmidfinder']['meta'] = {} - bacannot_summary[sample]['plasmid']['plasmidfinder']['meta']['database'] = results['Database'].unique().item() + db_arr = results['Database'].unique() + bacannot_summary[sample]['plasmid']['plasmidfinder']['meta']['database'] = db_arr.tolist() if len(db_arr) > 1 else db_arr.item() # number of plasmid annotations total_number = len(results['Contig'].unique()) From d8daa5945b97c95cb47e440410e4475497079aca Mon Sep 17 00:00:00 2001 From: fmalmeida Date: Wed, 19 Jul 2023 14:58:11 +0200 Subject: [PATCH 14/32] update version number --- conda.recipe/meta.yaml | 2 +- falmeida_py/version.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/conda.recipe/meta.yaml b/conda.recipe/meta.yaml index 985b5be..d3beb92 100644 --- a/conda.recipe/meta.yaml +++ b/conda.recipe/meta.yaml @@ -1,6 +1,6 @@ package: name: falmeida-py - version: '1.2.0' + version: '1.2.1' source: path: .. diff --git a/falmeida_py/version.py b/falmeida_py/version.py index e1ef2f0..b1a36f8 100644 --- a/falmeida_py/version.py +++ b/falmeida_py/version.py @@ -14,7 +14,7 @@ If not, see . """ -__version__ = '1.2.0' +__version__ = '1.2.1' def get_version(): return __version__ From 1c218fdee0e312f4cbf0fca2af901b8409878d0e Mon Sep 17 00:00:00 2001 From: fmalmeida Date: Wed, 19 Jul 2023 14:58:17 +0200 Subject: [PATCH 15/32] Update CHANGELOG.md --- CHANGELOG.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 6ddfafb..66bc07e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,6 +2,10 @@ Started only in version 0.5 +## v1.2.1 + +- Added a quick fix for plasmid finder results parsing, as results from gram-negative have only one database, but for gram-positive it has >1. + ## v0.5 ### hotfix From bd11078f2c16f7452f7609075553956c449f42a1 Mon Sep 17 00:00:00 2001 From: Felipe Marques de Almeida Date: Thu, 20 Jul 2023 07:14:58 +0000 Subject: [PATCH 16/32] add gitpod config --- .gitpod.yml | 14 ++++++++++++++ 1 file changed, 14 insertions(+) create mode 100644 .gitpod.yml diff --git a/.gitpod.yml b/.gitpod.yml new file mode 100644 index 0000000..a565aba --- /dev/null +++ b/.gitpod.yml @@ -0,0 +1,14 @@ +image: nfcore/gitpod:latest + +vscode: + extensions: # based on nf-core.nf-core-extensionpack + - codezombiech.gitignore # Language support for .gitignore files + # - cssho.vscode-svgviewer # SVG viewer + - esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code + - eamodio.gitlens # Quickly glimpse into whom, why, and when a line or code block was changed + - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files + - Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar + - mechatroner.rainbow-csv # Highlight columns in csv files in different colors + # - nextflow.nextflow # Nextflow syntax highlighting + - oderwat.indent-rainbow # Highlight indentation level + - streetsidesoftware.code-spell-checker # Spelling checker for source code \ No newline at end of file From db542739ca47479a31bde7f9ca43694f641a7b61 Mon Sep 17 00:00:00 2001 From: Felipe Almeida Date: Thu, 20 Jul 2023 04:50:02 -0300 Subject: [PATCH 17/32] update helps --- docs/align2subsetgbk_help.txt | 50 ++++++++++++++++++++++++++++++----- docs/help_message.txt | 31 +++++++++++++++++----- docs/splitgbk_help.txt | 44 +++++++++++++++++++++++++----- docs/tsv2markdown_help.txt | 46 +++++++++++++++++++++++++++----- 4 files changed, 147 insertions(+), 24 deletions(-) diff --git a/docs/align2subsetgbk_help.txt b/docs/align2subsetgbk_help.txt index 087e990..769c2b2 100644 --- a/docs/align2subsetgbk_help.txt +++ b/docs/align2subsetgbk_help.txt @@ -1,6 +1,44 @@ -Traceback (most recent call last): - File "/home/falmeida/Documents/GitHub/pythonScripts/falmeida-py-runner.py", line 18, in - from falmeida_py.__main__ import main - File "/home/falmeida/Documents/GitHub/pythonScripts/falmeida_py/__main__.py", line 47, in - from docopt import docopt -ModuleNotFoundError: No module named 'docopt' +A script meant to subset a genbank annotation file based on alignments against a query (Nucleotide) FASTA file + +--- +Copyright (C) 2020 Felipe Marques de Almeida (almeidafmarques@gmail.com) +License: Public Domain + +Usage: + falmeida-py align2subsetgbk [ -h|--help ] + falmeida-py align2subsetgbk [ --gbk --fasta --out --minid --mincov --culling_limit --extension ] + +Options: + -h --help Show this screen. + -g --gbk= Gbk file for subset + -f --fasta= FASTA (nucl) file for querying the gbk + -o --out= Gbk filtered output file [Default: out.gbk]. + --extension= Base pair length to extend the flank regions in the alignment [Default: 0]. + --minid= Min. Identity percentage for gene annotation [Default: 80]. + --mincov= Min. Covereage for gene annotation [Default: 80]. + --culling_limit= Blast culling_limit for best hit only [Default: 1]. +falmeida-py: a package to the simple distribution of my custom scripts. + +Copyright (C) 2020 Felipe Marques de Almeida (almeidafmarques@gmail.com) +License: Public Domain + +usage: + falmeida-py [ -h|--help ] [ -v|--version ] [ --license ] + falmeida-py [ -h|--help ] [ ... ] + +options: + -h --help Show this screen + -v --version Show version information + --license Show LEGAL LICENSE information + +commands: + tsv2markdown Command for rapid convertion of tsv or csv to markdown tables. + splitgbk Command to split multisequence genbank files into individual files. + align2subsetgbk Command to subset genbank files based on alignments to a FASTA file. + gbk2fasta Command to convert genbank files to fasta files. + blasts Command to execute automatized blast commands. + replace_fasta_seq Command to replace strings in a FASTA using defitinitions from a BED file + mpgap2csv Command to summarize main mpgap multiqc assembly statistics into a CSV file + bacannot2json Command to summarize main bacannot annotation results into JSON file + +Use: `falmeida-py -h` to get more help and see examples. diff --git a/docs/help_message.txt b/docs/help_message.txt index 087e990..6ed5318 100644 --- a/docs/help_message.txt +++ b/docs/help_message.txt @@ -1,6 +1,25 @@ -Traceback (most recent call last): - File "/home/falmeida/Documents/GitHub/pythonScripts/falmeida-py-runner.py", line 18, in - from falmeida_py.__main__ import main - File "/home/falmeida/Documents/GitHub/pythonScripts/falmeida_py/__main__.py", line 47, in - from docopt import docopt -ModuleNotFoundError: No module named 'docopt' +falmeida-py: a package to the simple distribution of my custom scripts. + +Copyright (C) 2020 Felipe Marques de Almeida (almeidafmarques@gmail.com) +License: Public Domain + +usage: + falmeida-py [ -h|--help ] [ -v|--version ] [ --license ] + falmeida-py [ -h|--help ] [ ... ] + +options: + -h --help Show this screen + -v --version Show version information + --license Show LEGAL LICENSE information + +commands: + tsv2markdown Command for rapid convertion of tsv or csv to markdown tables. + splitgbk Command to split multisequence genbank files into individual files. + align2subsetgbk Command to subset genbank files based on alignments to a FASTA file. + gbk2fasta Command to convert genbank files to fasta files. + blasts Command to execute automatized blast commands. + replace_fasta_seq Command to replace strings in a FASTA using defitinitions from a BED file + mpgap2csv Command to summarize main mpgap multiqc assembly statistics into a CSV file + bacannot2json Command to summarize main bacannot annotation results into JSON file + +Use: `falmeida-py -h` to get more help and see examples. diff --git a/docs/splitgbk_help.txt b/docs/splitgbk_help.txt index 087e990..f139033 100644 --- a/docs/splitgbk_help.txt +++ b/docs/splitgbk_help.txt @@ -1,6 +1,38 @@ -Traceback (most recent call last): - File "/home/falmeida/Documents/GitHub/pythonScripts/falmeida-py-runner.py", line 18, in - from falmeida_py.__main__ import main - File "/home/falmeida/Documents/GitHub/pythonScripts/falmeida_py/__main__.py", line 47, in - from docopt import docopt -ModuleNotFoundError: No module named 'docopt' +A very simple script to split multisequence genbank files into separate files +Copyright (C) 2020 Felipe Marques de Almeida (almeidafmarques@gmail.com) +License: Public Domain + +usage: + falmeida-py splitgbk + falmeida-py splitgbk [ -h|--help ] + falmeida-py splitgbk [ --gbk ] [ --outdir ] + +options: + -h --help Show this screen. + -g --gbk= Input genbank file to split into multiple individual files. + -o --outdir= Directory (must already exist) in which to write the splitted files [Default: ./]. +falmeida-py: a package to the simple distribution of my custom scripts. + +Copyright (C) 2020 Felipe Marques de Almeida (almeidafmarques@gmail.com) +License: Public Domain + +usage: + falmeida-py [ -h|--help ] [ -v|--version ] [ --license ] + falmeida-py [ -h|--help ] [ ... ] + +options: + -h --help Show this screen + -v --version Show version information + --license Show LEGAL LICENSE information + +commands: + tsv2markdown Command for rapid convertion of tsv or csv to markdown tables. + splitgbk Command to split multisequence genbank files into individual files. + align2subsetgbk Command to subset genbank files based on alignments to a FASTA file. + gbk2fasta Command to convert genbank files to fasta files. + blasts Command to execute automatized blast commands. + replace_fasta_seq Command to replace strings in a FASTA using defitinitions from a BED file + mpgap2csv Command to summarize main mpgap multiqc assembly statistics into a CSV file + bacannot2json Command to summarize main bacannot annotation results into JSON file + +Use: `falmeida-py -h` to get more help and see examples. diff --git a/docs/tsv2markdown_help.txt b/docs/tsv2markdown_help.txt index 087e990..0b2b685 100644 --- a/docs/tsv2markdown_help.txt +++ b/docs/tsv2markdown_help.txt @@ -1,6 +1,40 @@ -Traceback (most recent call last): - File "/home/falmeida/Documents/GitHub/pythonScripts/falmeida-py-runner.py", line 18, in - from falmeida_py.__main__ import main - File "/home/falmeida/Documents/GitHub/pythonScripts/falmeida_py/__main__.py", line 47, in - from docopt import docopt -ModuleNotFoundError: No module named 'docopt' +A simple script to convert tsv (or csv) files to markdown tables using tabulate! +Copyright (C) 2020 Felipe Marques de Almeida (almeidafmarques@gmail.com) +License: Public Domain + +usage: + falmeida-py tsv2markdown + falmeida-py tsv2markdown [ -h|--help ] + falmeida-py tsv2markdown [ --tsv --csv --header ] + +options: + -h --help Show this screen. + --tsv= Input tsv file to print as markdown table + --csv= Input csv file to print as markdown table + --header= If file does not have a header, set a + custom header. E.g. --header "Planet,R (km),mass (x 10^29 kg)". +falmeida-py: a package to the simple distribution of my custom scripts. + +Copyright (C) 2020 Felipe Marques de Almeida (almeidafmarques@gmail.com) +License: Public Domain + +usage: + falmeida-py [ -h|--help ] [ -v|--version ] [ --license ] + falmeida-py [ -h|--help ] [ ... ] + +options: + -h --help Show this screen + -v --version Show version information + --license Show LEGAL LICENSE information + +commands: + tsv2markdown Command for rapid convertion of tsv or csv to markdown tables. + splitgbk Command to split multisequence genbank files into individual files. + align2subsetgbk Command to subset genbank files based on alignments to a FASTA file. + gbk2fasta Command to convert genbank files to fasta files. + blasts Command to execute automatized blast commands. + replace_fasta_seq Command to replace strings in a FASTA using defitinitions from a BED file + mpgap2csv Command to summarize main mpgap multiqc assembly statistics into a CSV file + bacannot2json Command to summarize main bacannot annotation results into JSON file + +Use: `falmeida-py -h` to get more help and see examples. From a7d2f6f60696ef243e6a6daa49afa95fb5c4c4b8 Mon Sep 17 00:00:00 2001 From: Felipe Almeida Date: Sun, 23 Jul 2023 06:45:56 -0300 Subject: [PATCH 18/32] add check for file size and fix mob_suite subset --- falmeida_py/mges_function.py | 2 +- falmeida_py/plasmid_function.py | 8 ++++---- falmeida_py/resistance_function.py | 6 +++--- falmeida_py/virulence_function.py | 4 ++-- 4 files changed, 10 insertions(+), 10 deletions(-) diff --git a/falmeida_py/mges_function.py b/falmeida_py/mges_function.py index 035355c..42bdf57 100644 --- a/falmeida_py/mges_function.py +++ b/falmeida_py/mges_function.py @@ -19,7 +19,7 @@ def mges_stats(bacannot_summary): bacannot_summary[sample]['MGE'] = {} # integron_finder - if os.path.exists(f"{results_dir}/integron_finder/{sample}_integrons.gff"): + if os.path.exists(f"{results_dir}/integron_finder/{sample}_integrons.gff") and os.stat(f"{results_dir}/integron_finder/{sample}_integrons.gff").st_size > 0: # init integron_finder annotation dictionary bacannot_summary[sample]['MGE']['integron_finder'] = {} diff --git a/falmeida_py/plasmid_function.py b/falmeida_py/plasmid_function.py index d7cb62e..789aa9a 100644 --- a/falmeida_py/plasmid_function.py +++ b/falmeida_py/plasmid_function.py @@ -19,7 +19,7 @@ def plasmids_stats(bacannot_summary): bacannot_summary[sample]['plasmid'] = {} # platon - if os.path.exists(f"{results_dir}/plasmids/platon/{sample}.tsv"): + if os.path.exists(f"{results_dir}/plasmids/platon/{sample}.tsv") and os.stat(f"{results_dir}/plasmids/platon/{sample}.tsv").st_size > 0: # init platon annotation dictionary bacannot_summary[sample]['plasmid']['platon'] = {} @@ -47,7 +47,7 @@ def plasmids_stats(bacannot_summary): bacannot_summary[sample]['plasmid']['platon'][seq]['Conjugation'] = results.loc[results['ID'] == seq, '# Conjugation'].item() # plasmidfinder - if os.path.exists(f"{results_dir}/plasmids/plasmidfinder/results_tab.tsv"): + if os.path.exists(f"{results_dir}/plasmids/plasmidfinder/results_tab.tsv") and os.stat(f"{results_dir}/plasmids/plasmidfinder/results_tab.tsv").st_size > 0: # init platon annotation dictionary bacannot_summary[sample]['plasmid']['plasmidfinder'] = {} @@ -84,7 +84,7 @@ def plasmids_stats(bacannot_summary): bacannot_summary[sample]['plasmid']['plasmidfinder'][contig]['accession'] = row['Accession number'] # mob suite - if os.path.exists(f"{results_dir}/plasmids/mob_suite/{sample}_mobtyper_results.txt"): + if os.path.exists(f"{results_dir}/plasmids/mob_suite/{sample}_mobtyper_results.txt") and os.stat(f"{results_dir}/plasmids/mob_suite/{sample}_mobtyper_results.txt").st_size > 0: # init integron_finder annotation dictionary bacannot_summary[sample]['plasmid']['mob_suite'] = {} @@ -107,7 +107,7 @@ def plasmids_stats(bacannot_summary): for seq in [ str(x) for x in results['sample_id'].unique() ]: bacannot_summary[sample]['plasmid']['mob_suite'][seq] = {} - for index, row in results[results['sample_id'] == seq].reset_index().iterrows(): + for index, row in results[results['sample_id'].astype(str) == seq].reset_index().iterrows(): id = row['sample_id'] # they are the same for this result bacannot_summary[sample]['plasmid']['mob_suite'][seq][id] = {} bacannot_summary[sample]['plasmid']['mob_suite'][seq][id]['size'] = row['size'] diff --git a/falmeida_py/resistance_function.py b/falmeida_py/resistance_function.py index 7a4460a..3e1649e 100644 --- a/falmeida_py/resistance_function.py +++ b/falmeida_py/resistance_function.py @@ -33,7 +33,7 @@ def resistance_stats(bacannot_summary): ########### ### rgi ### ########### - if os.path.exists(f"{results_dir}/resistance/RGI/RGI_{sample}.txt"): + if os.path.exists(f"{results_dir}/resistance/RGI/RGI_{sample}.txt") and os.stat(f"{results_dir}/resistance/RGI/RGI_{sample}.txt").st_size > 0: # init rgi annotation dictionary bacannot_summary[sample]['resistance']['rgi'] = {} @@ -84,7 +84,7 @@ def resistance_stats(bacannot_summary): ##################### ### amrfinderplus ### ##################### - if os.path.exists(f"{results_dir}/resistance/AMRFinderPlus/AMRFinder_resistance-only.tsv"): + if os.path.exists(f"{results_dir}/resistance/AMRFinderPlus/AMRFinder_resistance-only.tsv") and os.stat(f"{results_dir}/resistance/AMRFinderPlus/AMRFinder_resistance-only.tsv").st_size > 0: # init amrfinderplus annotation dictionary bacannot_summary[sample]['resistance']['amrfinderplus'] = {} @@ -141,7 +141,7 @@ def resistance_stats(bacannot_summary): # # TODO: Include genomic coordinates info # - if os.path.exists(f"{results_dir}/resistance/resfinder/ResFinder_results_tab.txt"): + if os.path.exists(f"{results_dir}/resistance/resfinder/ResFinder_results_tab.txt") and os.stat(f"{results_dir}/resistance/resfinder/ResFinder_results_tab.txt").st_size > 0: # init resfinder annotation dictionary bacannot_summary[sample]['resistance']['resfinder'] = {} diff --git a/falmeida_py/virulence_function.py b/falmeida_py/virulence_function.py index 8656e30..91e912d 100644 --- a/falmeida_py/virulence_function.py +++ b/falmeida_py/virulence_function.py @@ -30,7 +30,7 @@ def virulence_stats(bacannot_summary): bacannot_summary[sample]['virulence'] = {} # vfdb - if os.path.exists(f"{results_dir}/virulence/vfdb/{sample}_vfdb_blastn_onGenes.summary.txt"): + if os.path.exists(f"{results_dir}/virulence/vfdb/{sample}_vfdb_blastn_onGenes.summary.txt") and os.stat(f"{results_dir}/virulence/vfdb/{sample}_vfdb_blastn_onGenes.summary.txt").st_size > 0: # init VFDB annotation dictionary bacannot_summary[sample]['virulence']['VFDB'] = {} @@ -73,7 +73,7 @@ def virulence_stats(bacannot_summary): bacannot_summary[sample]['virulence']['VFDB'][gene]['end'] = end # victors - if os.path.exists(f"{results_dir}/virulence/victors/{sample}_victors_blastp_onGenes.summary.txt"): + if os.path.exists(f"{results_dir}/virulence/victors/{sample}_victors_blastp_onGenes.summary.txt") and os.stat(f"{results_dir}/virulence/victors/{sample}_victors_blastp_onGenes.summary.txt").st_size > 0: # init victors annotation dictionary gff = bacannot_summary[sample]['virulence']['Victors'] = {} From 3510c4f0e66b7b0507248b4dca04dec2eacc9a8e Mon Sep 17 00:00:00 2001 From: Felipe Almeida Date: Sun, 23 Jul 2023 06:53:36 -0300 Subject: [PATCH 19/32] make MGE key only be created if integron_finder has results --- falmeida_py/mges_function.py | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/falmeida_py/mges_function.py b/falmeida_py/mges_function.py index 42bdf57..61311f8 100644 --- a/falmeida_py/mges_function.py +++ b/falmeida_py/mges_function.py @@ -14,13 +14,14 @@ def mges_stats(bacannot_summary): # load dir of samples' results results_dir = bacannot_summary[sample]['results_dir'] - - # init MGE annotation dictionary - bacannot_summary[sample]['MGE'] = {} # integron_finder if os.path.exists(f"{results_dir}/integron_finder/{sample}_integrons.gff") and os.stat(f"{results_dir}/integron_finder/{sample}_integrons.gff").st_size > 0: + # init MGE annotation dictionary + if 'MGE' not in bacannot_summary[sample]: + bacannot_summary[sample]['MGE'] = {} + # init integron_finder annotation dictionary bacannot_summary[sample]['MGE']['integron_finder'] = {} From bc0231a2bae081371585f4b3d5a1b0617c64aea3 Mon Sep 17 00:00:00 2001 From: Felipe Almeida Date: Sun, 23 Jul 2023 06:55:51 -0300 Subject: [PATCH 20/32] update versions and changelog --- CHANGELOG.md | 6 ++++++ conda.recipe/meta.yaml | 2 +- falmeida_py/version.py | 2 +- 3 files changed, 8 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 66bc07e..b718bd5 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,6 +2,12 @@ Started only in version 0.5 +## v1.2.2 + +- Added a file size check, only enter bacannot summary creation if results files are not empty +- Fixed mob_suite summary parsing (added .astype(str)) +- Moved MGE dict key generation for inside the integron_finder loop + ## v1.2.1 - Added a quick fix for plasmid finder results parsing, as results from gram-negative have only one database, but for gram-positive it has >1. diff --git a/conda.recipe/meta.yaml b/conda.recipe/meta.yaml index d3beb92..aef1d2b 100644 --- a/conda.recipe/meta.yaml +++ b/conda.recipe/meta.yaml @@ -1,6 +1,6 @@ package: name: falmeida-py - version: '1.2.1' + version: '1.2.2' source: path: .. diff --git a/falmeida_py/version.py b/falmeida_py/version.py index b1a36f8..a5b5600 100644 --- a/falmeida_py/version.py +++ b/falmeida_py/version.py @@ -14,7 +14,7 @@ If not, see . """ -__version__ = '1.2.1' +__version__ = '1.2.2' def get_version(): return __version__ From bc006d69a7a580c815238d0ce59117e2ef19e6fb Mon Sep 17 00:00:00 2001 From: Felipe Almeida Date: Thu, 14 Sep 2023 10:14:05 -0300 Subject: [PATCH 21/32] added ICEberg database blastp results --- falmeida_py/mges_function.py | 58 +++++++++++++++++++++++++++++++++++- 1 file changed, 57 insertions(+), 1 deletion(-) diff --git a/falmeida_py/mges_function.py b/falmeida_py/mges_function.py index 61311f8..7b1ed7b 100644 --- a/falmeida_py/mges_function.py +++ b/falmeida_py/mges_function.py @@ -3,6 +3,7 @@ ################################## import pandas as pd import os +from .utils import load_and_subset_gff #################################### ### check MGEs annotations stats ### @@ -14,6 +15,9 @@ def mges_stats(bacannot_summary): # load dir of samples' results results_dir = bacannot_summary[sample]['results_dir'] + + # load gff_file + gff_file = f"{results_dir}/gffs/{sample}.gff" # integron_finder if os.path.exists(f"{results_dir}/integron_finder/{sample}_integrons.gff") and os.stat(f"{results_dir}/integron_finder/{sample}_integrons.gff").st_size > 0: @@ -54,4 +58,56 @@ def mges_stats(bacannot_summary): bacannot_summary[sample]['MGE']['integron_finder'][seq][id]['end'] = row['end'] bacannot_summary[sample]['MGE']['integron_finder'][seq][id]['type'] = row['atts'].split(';')[1].split('=')[-1] bacannot_summary[sample]['MGE']['integron_finder'][seq][id]['source'] = row['source'] - bacannot_summary[sample]['MGE']['integron_finder'][seq][id]['product'] = row['type'] \ No newline at end of file + bacannot_summary[sample]['MGE']['integron_finder'][seq][id]['product'] = row['type'] + + # ICE database + ice_db_blastp = f"{results_dir}/ICEs/{sample}_iceberg_blastp_onGenes.summary.txt" + if os.path.exists(ice_db_blastp) and os.stat(ice_db_blastp).st_size > 0: + + # init MGE annotation dictionary + if 'MGE' not in bacannot_summary[sample]: + bacannot_summary[sample]['MGE'] = {} + + # init iceberg annotation dictionary + if 'ICE' not in bacannot_summary[sample]['MGE']: + bacannot_summary[sample]['MGE']['ICEberg'] = {} + + # init iceberg blastp annotation dictionary + bacannot_summary[sample]['MGE']['ICEberg']['blastp'] = {} + + # load integron_finder results + results = pd.read_csv( + ice_db_blastp, + sep='\t' + ) + + # load gff + gff = load_and_subset_gff(gff_file, 'source', 'ICE') + + # number of integron_finder annotations + total_number = len(results.index) + bacannot_summary[sample]['MGE']['ICEberg']['blastp']['total'] = total_number + + # per gene info + if int(results.shape[0]) > 0: + for seq in [ str(x) for x in results['SEQUENCE'].unique() ]: + + # details missing in output but available in gff + gff_row = gff[gff['attributes'].str.contains(seq)] + contig = gff_row['seq'].item() + start = gff_row['start'].item() + end = gff_row['end'].item() + + bacannot_summary[sample]['MGE']['ICEberg']['blastp'][seq] = {} + for index, row in results[results['SEQUENCE'] == seq].reset_index().iterrows(): + bacannot_summary[sample]['MGE']['ICEberg']['blastp'][seq][id] = {} + bacannot_summary[sample]['MGE']['ICEberg']['blastp'][seq][id]['id'] = row['ICEBERG_ID'] + bacannot_summary[sample]['MGE']['ICEberg']['blastp'][seq][id]['contig'] = contig + bacannot_summary[sample]['MGE']['ICEberg']['blastp'][seq][id]['start'] = start + bacannot_summary[sample]['MGE']['ICEberg']['blastp'][seq][id]['end'] = end + bacannot_summary[sample]['MGE']['ICEberg']['blastp'][seq][id]['accession'] = row['ACCESSION'] + bacannot_summary[sample]['MGE']['ICEberg']['blastp'][seq][id]['product'] = row['PRODUCT'] + bacannot_summary[sample]['MGE']['ICEberg']['blastp'][seq][id]['description'] = row['DESCRIPTION'] + bacannot_summary[sample]['MGE']['ICEberg']['blastp'][seq][id]['blast_start'] = row['START'] + bacannot_summary[sample]['MGE']['ICEberg']['blastp'][seq][id]['blast_end'] = row['END'] + bacannot_summary[sample]['MGE']['ICEberg']['blastp'][seq][id]['strand'] = row['STRAND'] \ No newline at end of file From 31a8ccf7bb88100be9a592b34158542da95b168e Mon Sep 17 00:00:00 2001 From: Felipe Almeida Date: Thu, 14 Sep 2023 11:35:55 -0300 Subject: [PATCH 22/32] added PHAST results to summary --- falmeida_py/mges_function.py | 82 ++++++++++++++++++++++++++++++------ 1 file changed, 69 insertions(+), 13 deletions(-) diff --git a/falmeida_py/mges_function.py b/falmeida_py/mges_function.py index 7b1ed7b..39014e0 100644 --- a/falmeida_py/mges_function.py +++ b/falmeida_py/mges_function.py @@ -60,7 +60,7 @@ def mges_stats(bacannot_summary): bacannot_summary[sample]['MGE']['integron_finder'][seq][id]['source'] = row['source'] bacannot_summary[sample]['MGE']['integron_finder'][seq][id]['product'] = row['type'] - # ICE database + # ICEberg database ice_db_blastp = f"{results_dir}/ICEs/{sample}_iceberg_blastp_onGenes.summary.txt" if os.path.exists(ice_db_blastp) and os.stat(ice_db_blastp).st_size > 0: @@ -82,7 +82,7 @@ def mges_stats(bacannot_summary): ) # load gff - gff = load_and_subset_gff(gff_file, 'source', 'ICE') + gff = load_and_subset_gff(gff_file, 'source', 'ICEberg') # number of integron_finder annotations total_number = len(results.index) @@ -100,14 +100,70 @@ def mges_stats(bacannot_summary): bacannot_summary[sample]['MGE']['ICEberg']['blastp'][seq] = {} for index, row in results[results['SEQUENCE'] == seq].reset_index().iterrows(): - bacannot_summary[sample]['MGE']['ICEberg']['blastp'][seq][id] = {} - bacannot_summary[sample]['MGE']['ICEberg']['blastp'][seq][id]['id'] = row['ICEBERG_ID'] - bacannot_summary[sample]['MGE']['ICEberg']['blastp'][seq][id]['contig'] = contig - bacannot_summary[sample]['MGE']['ICEberg']['blastp'][seq][id]['start'] = start - bacannot_summary[sample]['MGE']['ICEberg']['blastp'][seq][id]['end'] = end - bacannot_summary[sample]['MGE']['ICEberg']['blastp'][seq][id]['accession'] = row['ACCESSION'] - bacannot_summary[sample]['MGE']['ICEberg']['blastp'][seq][id]['product'] = row['PRODUCT'] - bacannot_summary[sample]['MGE']['ICEberg']['blastp'][seq][id]['description'] = row['DESCRIPTION'] - bacannot_summary[sample]['MGE']['ICEberg']['blastp'][seq][id]['blast_start'] = row['START'] - bacannot_summary[sample]['MGE']['ICEberg']['blastp'][seq][id]['blast_end'] = row['END'] - bacannot_summary[sample]['MGE']['ICEberg']['blastp'][seq][id]['strand'] = row['STRAND'] \ No newline at end of file + bacannot_summary[sample]['MGE']['ICEberg']['blastp'][seq] = {} + bacannot_summary[sample]['MGE']['ICEberg']['blastp'][seq]['id'] = row['ICEBERG_ID'] + bacannot_summary[sample]['MGE']['ICEberg']['blastp'][seq]['contig'] = contig + bacannot_summary[sample]['MGE']['ICEberg']['blastp'][seq]['start'] = start + bacannot_summary[sample]['MGE']['ICEberg']['blastp'][seq]['end'] = end + bacannot_summary[sample]['MGE']['ICEberg']['blastp'][seq]['accession'] = row['ACCESSION'] + bacannot_summary[sample]['MGE']['ICEberg']['blastp'][seq]['product'] = row['PRODUCT'] + bacannot_summary[sample]['MGE']['ICEberg']['blastp'][seq]['description'] = row['DESCRIPTION'] + bacannot_summary[sample]['MGE']['ICEberg']['blastp'][seq]['blast_start'] = row['START'] + bacannot_summary[sample]['MGE']['ICEberg']['blastp'][seq]['blast_end'] = row['END'] + bacannot_summary[sample]['MGE']['ICEberg']['blastp'][seq]['blast_identity'] = row['%IDENTITY'] + bacannot_summary[sample]['MGE']['ICEberg']['blastp'][seq]['blast_coverage'] = row['%COVERAGE'] + bacannot_summary[sample]['MGE']['ICEberg']['blastp'][seq]['strand'] = row['STRAND'] + + # PHAST database + phast_db_blastp = f"{results_dir}/prophages/phast_db/{sample}_phast_blastp_onGenes.summary.txt" + if os.path.exists(phast_db_blastp) and os.stat(phast_db_blastp).st_size > 0: + + # init MGE annotation dictionary + if 'MGE' not in bacannot_summary[sample]: + bacannot_summary[sample]['MGE'] = {} + + # init phast annotation dictionary + if 'ICE' not in bacannot_summary[sample]['MGE']: + bacannot_summary[sample]['MGE']['PHAST'] = {} + + # init phast blastp annotation dictionary + bacannot_summary[sample]['MGE']['PHAST']['blastp'] = {} + + # load integron_finder results + results = pd.read_csv( + phast_db_blastp, + sep='\t' + ) + + # load gff + gff = load_and_subset_gff(gff_file, 'source', 'PHAST') + + # number of integron_finder annotations + total_number = len(results.index) + bacannot_summary[sample]['MGE']['PHAST']['blastp']['total'] = total_number + + # per gene info + if int(results.shape[0]) > 0: + for seq in [ str(x) for x in results['SEQUENCE'].unique() ]: + + # details missing in output but available in gff + gff_row = gff[gff['attributes'].str.contains(seq)] + contig = gff_row['seq'].item() + start = gff_row['start'].item() + end = gff_row['end'].item() + + bacannot_summary[sample]['MGE']['PHAST']['blastp'][seq] = {} + for index, row in results[results['SEQUENCE'] == seq].reset_index().iterrows(): + bacannot_summary[sample]['MGE']['PHAST']['blastp'][seq] = {} + bacannot_summary[sample]['MGE']['PHAST']['blastp'][seq]['id'] = row['PHAST_ID'] + bacannot_summary[sample]['MGE']['PHAST']['blastp'][seq]['contig'] = contig + bacannot_summary[sample]['MGE']['PHAST']['blastp'][seq]['start'] = start + bacannot_summary[sample]['MGE']['PHAST']['blastp'][seq]['end'] = end + bacannot_summary[sample]['MGE']['PHAST']['blastp'][seq]['accession'] = row['ACCESSION'] + bacannot_summary[sample]['MGE']['PHAST']['blastp'][seq]['gene'] = row['GENE'] + bacannot_summary[sample]['MGE']['PHAST']['blastp'][seq]['description'] = row['DESCRIPTION'] + bacannot_summary[sample]['MGE']['PHAST']['blastp'][seq]['blast_start'] = row['START'] + bacannot_summary[sample]['MGE']['PHAST']['blastp'][seq]['blast_end'] = row['END'] + bacannot_summary[sample]['MGE']['PHAST']['blastp'][seq]['blast_identity'] = row['%IDENTITY'] + bacannot_summary[sample]['MGE']['PHAST']['blastp'][seq]['blast_coverage'] = row['%COVERAGE'] + bacannot_summary[sample]['MGE']['PHAST']['blastp'][seq]['strand'] = row['STRAND'] \ No newline at end of file From 13ee380f72eca34466ab11bf27ce5aab4648cd08 Mon Sep 17 00:00:00 2001 From: Felipe Almeida Date: Thu, 14 Sep 2023 11:37:37 -0300 Subject: [PATCH 23/32] update version --- CHANGELOG.md | 4 ++++ conda.recipe/meta.yaml | 2 +- falmeida_py/version.py | 2 +- 3 files changed, 6 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index b718bd5..70413f1 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,6 +2,10 @@ Started only in version 0.5 +## v1.2.3 + +- Added ICEberg and PHAST results to bacannot json summary file + ## v1.2.2 - Added a file size check, only enter bacannot summary creation if results files are not empty diff --git a/conda.recipe/meta.yaml b/conda.recipe/meta.yaml index aef1d2b..18f3645 100644 --- a/conda.recipe/meta.yaml +++ b/conda.recipe/meta.yaml @@ -1,6 +1,6 @@ package: name: falmeida-py - version: '1.2.2' + version: '1.2.3' source: path: .. diff --git a/falmeida_py/version.py b/falmeida_py/version.py index a5b5600..304580c 100644 --- a/falmeida_py/version.py +++ b/falmeida_py/version.py @@ -14,7 +14,7 @@ If not, see . """ -__version__ = '1.2.2' +__version__ = '1.2.3' def get_version(): return __version__ From d5c04f230ac0148f3d4207e344fb995c993fc3db Mon Sep 17 00:00:00 2001 From: fmalmeida Date: Sun, 17 Sep 2023 20:57:07 +0200 Subject: [PATCH 24/32] Create pyproject.toml --- pyproject.toml | 6 ++++++ 1 file changed, 6 insertions(+) create mode 100644 pyproject.toml diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 0000000..7d4b7be --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,6 @@ +[project] +name="falmeida-py" +version="1.2.3" +description="A python package of my (Felipe M. Almeida) personal python scripts" +requires-python=">=3.7" +readme="README.md" From c579d29b28edc1d84292e8f368198fba5f695e5b Mon Sep 17 00:00:00 2001 From: fmalmeida Date: Mon, 18 Sep 2023 22:08:33 +0200 Subject: [PATCH 25/32] fix requirements --- build_conda.sh | 2 +- pyproject.toml | 6 ------ 2 files changed, 1 insertion(+), 7 deletions(-) delete mode 100644 pyproject.toml diff --git a/build_conda.sh b/build_conda.sh index ea63aba..76fc21a 100644 --- a/build_conda.sh +++ b/build_conda.sh @@ -9,7 +9,7 @@ conda convert -p osx-64 $(find build -name "falmeida-py*.tar.bz2") # upload osx anaconda upload $(find osx-64 -name "falmeida-py*.tar.bz2") --force -( cd build && anaconda upload $(find linux-64 -name "falmeida-py*.tar.bz2") --force ) +anaconda upload $(find build/linux-64 -name "falmeida-py*.tar.bz2") --force # rm dirs rm -rf build osx-64 diff --git a/pyproject.toml b/pyproject.toml deleted file mode 100644 index 7d4b7be..0000000 --- a/pyproject.toml +++ /dev/null @@ -1,6 +0,0 @@ -[project] -name="falmeida-py" -version="1.2.3" -description="A python package of my (Felipe M. Almeida) personal python scripts" -requires-python=">=3.7" -readme="README.md" From f27b5995644ed1bbdeea53ecc9b7079cd1337c56 Mon Sep 17 00:00:00 2001 From: fmalmeida Date: Mon, 18 Sep 2023 22:10:55 +0200 Subject: [PATCH 26/32] Update requirements.txt --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index baf0574..eff09bb 100644 --- a/requirements.txt +++ b/requirements.txt @@ -4,4 +4,4 @@ tabulate biopython simplejson importlib_metadata -yaml +pyyaml From 976a3d411d26e959262fe3c748cbb1859cb03579 Mon Sep 17 00:00:00 2001 From: fmalmeida Date: Mon, 18 Sep 2023 22:53:56 +0200 Subject: [PATCH 27/32] Update meta.yaml --- conda.recipe/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conda.recipe/meta.yaml b/conda.recipe/meta.yaml index 18f3645..2dfa0db 100644 --- a/conda.recipe/meta.yaml +++ b/conda.recipe/meta.yaml @@ -7,7 +7,7 @@ source: build: number: 0 - script: python setup.py install --single-version-externally-managed --record=record.txt + script: pip install . entry_points: - processrcmfolder = uconnrcmpy.dataprocessing:process_folder From 4e34f207810622b26d10b56f8290a9d54b92d2bd Mon Sep 17 00:00:00 2001 From: fmalmeida Date: Mon, 16 Oct 2023 20:58:37 +0200 Subject: [PATCH 28/32] start bug fix --- build_conda.sh | 1 + conda.recipe/meta.yaml | 2 +- docs/align2subsetgbk_help.txt | 50 ++++----------------------- docs/help_message.txt | 31 ++++------------- docs/splitgbk_help.txt | 44 ++++------------------- docs/tsv2markdown_help.txt | 46 ++++-------------------- falmeida_py/general_stats_function.py | 8 ++--- falmeida_py/version.py | 2 +- 8 files changed, 31 insertions(+), 153 deletions(-) diff --git a/build_conda.sh b/build_conda.sh index 76fc21a..d3d0571 100644 --- a/build_conda.sh +++ b/build_conda.sh @@ -9,6 +9,7 @@ conda convert -p osx-64 $(find build -name "falmeida-py*.tar.bz2") # upload osx anaconda upload $(find osx-64 -name "falmeida-py*.tar.bz2") --force +sleep 140 anaconda upload $(find build/linux-64 -name "falmeida-py*.tar.bz2") --force # rm dirs diff --git a/conda.recipe/meta.yaml b/conda.recipe/meta.yaml index 2dfa0db..b1e862a 100644 --- a/conda.recipe/meta.yaml +++ b/conda.recipe/meta.yaml @@ -1,6 +1,6 @@ package: name: falmeida-py - version: '1.2.3' + version: '1.2.4' source: path: .. diff --git a/docs/align2subsetgbk_help.txt b/docs/align2subsetgbk_help.txt index 769c2b2..087e990 100644 --- a/docs/align2subsetgbk_help.txt +++ b/docs/align2subsetgbk_help.txt @@ -1,44 +1,6 @@ -A script meant to subset a genbank annotation file based on alignments against a query (Nucleotide) FASTA file - ---- -Copyright (C) 2020 Felipe Marques de Almeida (almeidafmarques@gmail.com) -License: Public Domain - -Usage: - falmeida-py align2subsetgbk [ -h|--help ] - falmeida-py align2subsetgbk [ --gbk --fasta --out --minid --mincov --culling_limit --extension ] - -Options: - -h --help Show this screen. - -g --gbk= Gbk file for subset - -f --fasta= FASTA (nucl) file for querying the gbk - -o --out= Gbk filtered output file [Default: out.gbk]. - --extension= Base pair length to extend the flank regions in the alignment [Default: 0]. - --minid= Min. Identity percentage for gene annotation [Default: 80]. - --mincov= Min. Covereage for gene annotation [Default: 80]. - --culling_limit= Blast culling_limit for best hit only [Default: 1]. -falmeida-py: a package to the simple distribution of my custom scripts. - -Copyright (C) 2020 Felipe Marques de Almeida (almeidafmarques@gmail.com) -License: Public Domain - -usage: - falmeida-py [ -h|--help ] [ -v|--version ] [ --license ] - falmeida-py [ -h|--help ] [ ... ] - -options: - -h --help Show this screen - -v --version Show version information - --license Show LEGAL LICENSE information - -commands: - tsv2markdown Command for rapid convertion of tsv or csv to markdown tables. - splitgbk Command to split multisequence genbank files into individual files. - align2subsetgbk Command to subset genbank files based on alignments to a FASTA file. - gbk2fasta Command to convert genbank files to fasta files. - blasts Command to execute automatized blast commands. - replace_fasta_seq Command to replace strings in a FASTA using defitinitions from a BED file - mpgap2csv Command to summarize main mpgap multiqc assembly statistics into a CSV file - bacannot2json Command to summarize main bacannot annotation results into JSON file - -Use: `falmeida-py -h` to get more help and see examples. +Traceback (most recent call last): + File "/home/falmeida/Documents/GitHub/pythonScripts/falmeida-py-runner.py", line 18, in + from falmeida_py.__main__ import main + File "/home/falmeida/Documents/GitHub/pythonScripts/falmeida_py/__main__.py", line 47, in + from docopt import docopt +ModuleNotFoundError: No module named 'docopt' diff --git a/docs/help_message.txt b/docs/help_message.txt index 6ed5318..087e990 100644 --- a/docs/help_message.txt +++ b/docs/help_message.txt @@ -1,25 +1,6 @@ -falmeida-py: a package to the simple distribution of my custom scripts. - -Copyright (C) 2020 Felipe Marques de Almeida (almeidafmarques@gmail.com) -License: Public Domain - -usage: - falmeida-py [ -h|--help ] [ -v|--version ] [ --license ] - falmeida-py [ -h|--help ] [ ... ] - -options: - -h --help Show this screen - -v --version Show version information - --license Show LEGAL LICENSE information - -commands: - tsv2markdown Command for rapid convertion of tsv or csv to markdown tables. - splitgbk Command to split multisequence genbank files into individual files. - align2subsetgbk Command to subset genbank files based on alignments to a FASTA file. - gbk2fasta Command to convert genbank files to fasta files. - blasts Command to execute automatized blast commands. - replace_fasta_seq Command to replace strings in a FASTA using defitinitions from a BED file - mpgap2csv Command to summarize main mpgap multiqc assembly statistics into a CSV file - bacannot2json Command to summarize main bacannot annotation results into JSON file - -Use: `falmeida-py -h` to get more help and see examples. +Traceback (most recent call last): + File "/home/falmeida/Documents/GitHub/pythonScripts/falmeida-py-runner.py", line 18, in + from falmeida_py.__main__ import main + File "/home/falmeida/Documents/GitHub/pythonScripts/falmeida_py/__main__.py", line 47, in + from docopt import docopt +ModuleNotFoundError: No module named 'docopt' diff --git a/docs/splitgbk_help.txt b/docs/splitgbk_help.txt index f139033..087e990 100644 --- a/docs/splitgbk_help.txt +++ b/docs/splitgbk_help.txt @@ -1,38 +1,6 @@ -A very simple script to split multisequence genbank files into separate files -Copyright (C) 2020 Felipe Marques de Almeida (almeidafmarques@gmail.com) -License: Public Domain - -usage: - falmeida-py splitgbk - falmeida-py splitgbk [ -h|--help ] - falmeida-py splitgbk [ --gbk ] [ --outdir ] - -options: - -h --help Show this screen. - -g --gbk= Input genbank file to split into multiple individual files. - -o --outdir= Directory (must already exist) in which to write the splitted files [Default: ./]. -falmeida-py: a package to the simple distribution of my custom scripts. - -Copyright (C) 2020 Felipe Marques de Almeida (almeidafmarques@gmail.com) -License: Public Domain - -usage: - falmeida-py [ -h|--help ] [ -v|--version ] [ --license ] - falmeida-py [ -h|--help ] [ ... ] - -options: - -h --help Show this screen - -v --version Show version information - --license Show LEGAL LICENSE information - -commands: - tsv2markdown Command for rapid convertion of tsv or csv to markdown tables. - splitgbk Command to split multisequence genbank files into individual files. - align2subsetgbk Command to subset genbank files based on alignments to a FASTA file. - gbk2fasta Command to convert genbank files to fasta files. - blasts Command to execute automatized blast commands. - replace_fasta_seq Command to replace strings in a FASTA using defitinitions from a BED file - mpgap2csv Command to summarize main mpgap multiqc assembly statistics into a CSV file - bacannot2json Command to summarize main bacannot annotation results into JSON file - -Use: `falmeida-py -h` to get more help and see examples. +Traceback (most recent call last): + File "/home/falmeida/Documents/GitHub/pythonScripts/falmeida-py-runner.py", line 18, in + from falmeida_py.__main__ import main + File "/home/falmeida/Documents/GitHub/pythonScripts/falmeida_py/__main__.py", line 47, in + from docopt import docopt +ModuleNotFoundError: No module named 'docopt' diff --git a/docs/tsv2markdown_help.txt b/docs/tsv2markdown_help.txt index 0b2b685..087e990 100644 --- a/docs/tsv2markdown_help.txt +++ b/docs/tsv2markdown_help.txt @@ -1,40 +1,6 @@ -A simple script to convert tsv (or csv) files to markdown tables using tabulate! -Copyright (C) 2020 Felipe Marques de Almeida (almeidafmarques@gmail.com) -License: Public Domain - -usage: - falmeida-py tsv2markdown - falmeida-py tsv2markdown [ -h|--help ] - falmeida-py tsv2markdown [ --tsv --csv --header ] - -options: - -h --help Show this screen. - --tsv= Input tsv file to print as markdown table - --csv= Input csv file to print as markdown table - --header= If file does not have a header, set a - custom header. E.g. --header "Planet,R (km),mass (x 10^29 kg)". -falmeida-py: a package to the simple distribution of my custom scripts. - -Copyright (C) 2020 Felipe Marques de Almeida (almeidafmarques@gmail.com) -License: Public Domain - -usage: - falmeida-py [ -h|--help ] [ -v|--version ] [ --license ] - falmeida-py [ -h|--help ] [ ... ] - -options: - -h --help Show this screen - -v --version Show version information - --license Show LEGAL LICENSE information - -commands: - tsv2markdown Command for rapid convertion of tsv or csv to markdown tables. - splitgbk Command to split multisequence genbank files into individual files. - align2subsetgbk Command to subset genbank files based on alignments to a FASTA file. - gbk2fasta Command to convert genbank files to fasta files. - blasts Command to execute automatized blast commands. - replace_fasta_seq Command to replace strings in a FASTA using defitinitions from a BED file - mpgap2csv Command to summarize main mpgap multiqc assembly statistics into a CSV file - bacannot2json Command to summarize main bacannot annotation results into JSON file - -Use: `falmeida-py -h` to get more help and see examples. +Traceback (most recent call last): + File "/home/falmeida/Documents/GitHub/pythonScripts/falmeida-py-runner.py", line 18, in + from falmeida_py.__main__ import main + File "/home/falmeida/Documents/GitHub/pythonScripts/falmeida_py/__main__.py", line 47, in + from docopt import docopt +ModuleNotFoundError: No module named 'docopt' diff --git a/falmeida_py/general_stats_function.py b/falmeida_py/general_stats_function.py index 74e0893..80e2590 100644 --- a/falmeida_py/general_stats_function.py +++ b/falmeida_py/general_stats_function.py @@ -37,10 +37,10 @@ def general_stats(bacannot_summary): # save annotation stats bacannot_summary[sample]['general_annotation'] = {} bacannot_summary[sample]['general_annotation']['mlst'] = str(mlst_results[2].item()).replace('-', 'null') - bacannot_summary[sample]['general_annotation']['cds'] = general_results['CDS'] - bacannot_summary[sample]['general_annotation']['rrna'] = general_results['rRNA'] - bacannot_summary[sample]['general_annotation']['trna'] = general_results['tRNA'] - bacannot_summary[sample]['general_annotation']['tmrna'] = general_results['tmRNA'] + bacannot_summary[sample]['general_annotation']['cds'] = general_results.get('CDS', 0) + bacannot_summary[sample]['general_annotation']['rrna'] = general_results.get('rRNA', 0) + bacannot_summary[sample]['general_annotation']['trna'] = general_results.get('tRNA', 0) + bacannot_summary[sample]['general_annotation']['tmrna'] = general_results.get('tmRNA', 0) bacannot_summary[sample]['general_annotation']['closest_reference'] = {} bacannot_summary[sample]['general_annotation']['closest_reference']['strain'] = refseq_masher_results.head(1)['top_taxonomy_name'].item() diff --git a/falmeida_py/version.py b/falmeida_py/version.py index 304580c..e524e2d 100644 --- a/falmeida_py/version.py +++ b/falmeida_py/version.py @@ -14,7 +14,7 @@ If not, see . """ -__version__ = '1.2.3' +__version__ = '1.2.4' def get_version(): return __version__ From 48913d138568c797913845cc45854b6c8a96b730 Mon Sep 17 00:00:00 2001 From: Felipe Almeida Date: Sat, 28 Oct 2023 12:54:23 -0300 Subject: [PATCH 29/32] updated help --- docs/align2subsetgbk_help.txt | 50 ++++++++++++++++++++++++++++++----- docs/help_message.txt | 31 +++++++++++++++++----- docs/splitgbk_help.txt | 44 +++++++++++++++++++++++++----- docs/tsv2markdown_help.txt | 46 +++++++++++++++++++++++++++----- 4 files changed, 147 insertions(+), 24 deletions(-) diff --git a/docs/align2subsetgbk_help.txt b/docs/align2subsetgbk_help.txt index 087e990..769c2b2 100644 --- a/docs/align2subsetgbk_help.txt +++ b/docs/align2subsetgbk_help.txt @@ -1,6 +1,44 @@ -Traceback (most recent call last): - File "/home/falmeida/Documents/GitHub/pythonScripts/falmeida-py-runner.py", line 18, in - from falmeida_py.__main__ import main - File "/home/falmeida/Documents/GitHub/pythonScripts/falmeida_py/__main__.py", line 47, in - from docopt import docopt -ModuleNotFoundError: No module named 'docopt' +A script meant to subset a genbank annotation file based on alignments against a query (Nucleotide) FASTA file + +--- +Copyright (C) 2020 Felipe Marques de Almeida (almeidafmarques@gmail.com) +License: Public Domain + +Usage: + falmeida-py align2subsetgbk [ -h|--help ] + falmeida-py align2subsetgbk [ --gbk --fasta --out --minid --mincov --culling_limit --extension ] + +Options: + -h --help Show this screen. + -g --gbk= Gbk file for subset + -f --fasta= FASTA (nucl) file for querying the gbk + -o --out= Gbk filtered output file [Default: out.gbk]. + --extension= Base pair length to extend the flank regions in the alignment [Default: 0]. + --minid= Min. Identity percentage for gene annotation [Default: 80]. + --mincov= Min. Covereage for gene annotation [Default: 80]. + --culling_limit= Blast culling_limit for best hit only [Default: 1]. +falmeida-py: a package to the simple distribution of my custom scripts. + +Copyright (C) 2020 Felipe Marques de Almeida (almeidafmarques@gmail.com) +License: Public Domain + +usage: + falmeida-py [ -h|--help ] [ -v|--version ] [ --license ] + falmeida-py [ -h|--help ] [ ... ] + +options: + -h --help Show this screen + -v --version Show version information + --license Show LEGAL LICENSE information + +commands: + tsv2markdown Command for rapid convertion of tsv or csv to markdown tables. + splitgbk Command to split multisequence genbank files into individual files. + align2subsetgbk Command to subset genbank files based on alignments to a FASTA file. + gbk2fasta Command to convert genbank files to fasta files. + blasts Command to execute automatized blast commands. + replace_fasta_seq Command to replace strings in a FASTA using defitinitions from a BED file + mpgap2csv Command to summarize main mpgap multiqc assembly statistics into a CSV file + bacannot2json Command to summarize main bacannot annotation results into JSON file + +Use: `falmeida-py -h` to get more help and see examples. diff --git a/docs/help_message.txt b/docs/help_message.txt index 087e990..6ed5318 100644 --- a/docs/help_message.txt +++ b/docs/help_message.txt @@ -1,6 +1,25 @@ -Traceback (most recent call last): - File "/home/falmeida/Documents/GitHub/pythonScripts/falmeida-py-runner.py", line 18, in - from falmeida_py.__main__ import main - File "/home/falmeida/Documents/GitHub/pythonScripts/falmeida_py/__main__.py", line 47, in - from docopt import docopt -ModuleNotFoundError: No module named 'docopt' +falmeida-py: a package to the simple distribution of my custom scripts. + +Copyright (C) 2020 Felipe Marques de Almeida (almeidafmarques@gmail.com) +License: Public Domain + +usage: + falmeida-py [ -h|--help ] [ -v|--version ] [ --license ] + falmeida-py [ -h|--help ] [ ... ] + +options: + -h --help Show this screen + -v --version Show version information + --license Show LEGAL LICENSE information + +commands: + tsv2markdown Command for rapid convertion of tsv or csv to markdown tables. + splitgbk Command to split multisequence genbank files into individual files. + align2subsetgbk Command to subset genbank files based on alignments to a FASTA file. + gbk2fasta Command to convert genbank files to fasta files. + blasts Command to execute automatized blast commands. + replace_fasta_seq Command to replace strings in a FASTA using defitinitions from a BED file + mpgap2csv Command to summarize main mpgap multiqc assembly statistics into a CSV file + bacannot2json Command to summarize main bacannot annotation results into JSON file + +Use: `falmeida-py -h` to get more help and see examples. diff --git a/docs/splitgbk_help.txt b/docs/splitgbk_help.txt index 087e990..f139033 100644 --- a/docs/splitgbk_help.txt +++ b/docs/splitgbk_help.txt @@ -1,6 +1,38 @@ -Traceback (most recent call last): - File "/home/falmeida/Documents/GitHub/pythonScripts/falmeida-py-runner.py", line 18, in - from falmeida_py.__main__ import main - File "/home/falmeida/Documents/GitHub/pythonScripts/falmeida_py/__main__.py", line 47, in - from docopt import docopt -ModuleNotFoundError: No module named 'docopt' +A very simple script to split multisequence genbank files into separate files +Copyright (C) 2020 Felipe Marques de Almeida (almeidafmarques@gmail.com) +License: Public Domain + +usage: + falmeida-py splitgbk + falmeida-py splitgbk [ -h|--help ] + falmeida-py splitgbk [ --gbk ] [ --outdir ] + +options: + -h --help Show this screen. + -g --gbk= Input genbank file to split into multiple individual files. + -o --outdir= Directory (must already exist) in which to write the splitted files [Default: ./]. +falmeida-py: a package to the simple distribution of my custom scripts. + +Copyright (C) 2020 Felipe Marques de Almeida (almeidafmarques@gmail.com) +License: Public Domain + +usage: + falmeida-py [ -h|--help ] [ -v|--version ] [ --license ] + falmeida-py [ -h|--help ] [ ... ] + +options: + -h --help Show this screen + -v --version Show version information + --license Show LEGAL LICENSE information + +commands: + tsv2markdown Command for rapid convertion of tsv or csv to markdown tables. + splitgbk Command to split multisequence genbank files into individual files. + align2subsetgbk Command to subset genbank files based on alignments to a FASTA file. + gbk2fasta Command to convert genbank files to fasta files. + blasts Command to execute automatized blast commands. + replace_fasta_seq Command to replace strings in a FASTA using defitinitions from a BED file + mpgap2csv Command to summarize main mpgap multiqc assembly statistics into a CSV file + bacannot2json Command to summarize main bacannot annotation results into JSON file + +Use: `falmeida-py -h` to get more help and see examples. diff --git a/docs/tsv2markdown_help.txt b/docs/tsv2markdown_help.txt index 087e990..0b2b685 100644 --- a/docs/tsv2markdown_help.txt +++ b/docs/tsv2markdown_help.txt @@ -1,6 +1,40 @@ -Traceback (most recent call last): - File "/home/falmeida/Documents/GitHub/pythonScripts/falmeida-py-runner.py", line 18, in - from falmeida_py.__main__ import main - File "/home/falmeida/Documents/GitHub/pythonScripts/falmeida_py/__main__.py", line 47, in - from docopt import docopt -ModuleNotFoundError: No module named 'docopt' +A simple script to convert tsv (or csv) files to markdown tables using tabulate! +Copyright (C) 2020 Felipe Marques de Almeida (almeidafmarques@gmail.com) +License: Public Domain + +usage: + falmeida-py tsv2markdown + falmeida-py tsv2markdown [ -h|--help ] + falmeida-py tsv2markdown [ --tsv --csv --header ] + +options: + -h --help Show this screen. + --tsv= Input tsv file to print as markdown table + --csv= Input csv file to print as markdown table + --header= If file does not have a header, set a + custom header. E.g. --header "Planet,R (km),mass (x 10^29 kg)". +falmeida-py: a package to the simple distribution of my custom scripts. + +Copyright (C) 2020 Felipe Marques de Almeida (almeidafmarques@gmail.com) +License: Public Domain + +usage: + falmeida-py [ -h|--help ] [ -v|--version ] [ --license ] + falmeida-py [ -h|--help ] [ ... ] + +options: + -h --help Show this screen + -v --version Show version information + --license Show LEGAL LICENSE information + +commands: + tsv2markdown Command for rapid convertion of tsv or csv to markdown tables. + splitgbk Command to split multisequence genbank files into individual files. + align2subsetgbk Command to subset genbank files based on alignments to a FASTA file. + gbk2fasta Command to convert genbank files to fasta files. + blasts Command to execute automatized blast commands. + replace_fasta_seq Command to replace strings in a FASTA using defitinitions from a BED file + mpgap2csv Command to summarize main mpgap multiqc assembly statistics into a CSV file + bacannot2json Command to summarize main bacannot annotation results into JSON file + +Use: `falmeida-py -h` to get more help and see examples. From 705250f2e0b0c20a5ec1094de84979aad07290f8 Mon Sep 17 00:00:00 2001 From: Felipe Marques de Almeida Date: Fri, 3 Nov 2023 13:53:34 -0400 Subject: [PATCH 30/32] Update resistance_function.py --- falmeida_py/resistance_function.py | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/falmeida_py/resistance_function.py b/falmeida_py/resistance_function.py index 3e1649e..4b92adb 100644 --- a/falmeida_py/resistance_function.py +++ b/falmeida_py/resistance_function.py @@ -130,10 +130,13 @@ def resistance_stats(bacannot_summary): # # check for rgi orthologies # - if gene in bacannot_summary[sample]['resistance']['rgi']: - bacannot_summary[sample]['resistance']['amrfinderplus'][gene]['card_aro'] = bacannot_summary[sample]['resistance']['rgi'][gene]['card_aro'] - else: - bacannot_summary[sample]['resistance']['amrfinderplus'][gene]['card_aro'] = None + try: + if gene in bacannot_summary[sample]['resistance']['rgi']: + bacannot_summary[sample]['resistance']['amrfinderplus'][gene]['card_aro'] = bacannot_summary[sample]['resistance']['rgi'][gene]['card_aro'] + else: + bacannot_summary[sample]['resistance']['amrfinderplus'][gene]['card_aro'] = None + except: + bacannot_summary[sample]['resistance']['amrfinderplus'][gene]['card_aro'] = None ################# ### resfinder ### From c03b9f0753d51c0c698fec125822a72a9c0766da Mon Sep 17 00:00:00 2001 From: Felipe Marques de Almeida Date: Fri, 3 Nov 2023 13:56:22 -0400 Subject: [PATCH 31/32] Update resistance_function.py --- falmeida_py/resistance_function.py | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/falmeida_py/resistance_function.py b/falmeida_py/resistance_function.py index 4b92adb..7f7ff01 100644 --- a/falmeida_py/resistance_function.py +++ b/falmeida_py/resistance_function.py @@ -180,7 +180,10 @@ def resistance_stats(bacannot_summary): # # check for rgi orthologies # - if gene in bacannot_summary[sample]['resistance']['rgi']: - bacannot_summary[sample]['resistance']['resfinder'][gene]['card_aro'] = bacannot_summary[sample]['resistance']['rgi'][gene]['card_aro'] - else: - bacannot_summary[sample]['resistance']['resfinder'][gene]['card_aro'] = None + try: + if gene in bacannot_summary[sample]['resistance']['rgi']: + bacannot_summary[sample]['resistance']['resfinder'][gene]['card_aro'] = bacannot_summary[sample]['resistance']['rgi'][gene]['card_aro'] + else: + bacannot_summary[sample]['resistance']['resfinder'][gene]['card_aro'] = None + except: + bacannot_summary[sample]['resistance']['resfinder'][gene]['card_aro'] = None From 183693638254cb81c2865b202d76c31e83144fc2 Mon Sep 17 00:00:00 2001 From: Felipe Almeida Date: Tue, 7 Nov 2023 13:05:40 -0300 Subject: [PATCH 32/32] Fix help message --- falmeida_py/__main__.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/falmeida_py/__main__.py b/falmeida_py/__main__.py index 85208f7..4b94bba 100644 --- a/falmeida_py/__main__.py +++ b/falmeida_py/__main__.py @@ -241,8 +241,8 @@ def main(): ####################################### ### Without commands nor parameters ### ####################################### - else: - print(usage.strip()) + elif not arguments['']: + print(usage.strip()) ## Calling main if __name__ == '__main__':