1. Get a list of files you want to upload (see get-files-to-upload/)
2. Download the files in the list (see curl-all.py)
3. Unzip downloaded files (if needed)

cd downloads
gunzip *.gz

1. Use data_set.py to create individual data sets (see python data_set.py --help). You will need a Quilt username and password. Or use batch.py to create multiple data sets.

python data_set.py
  -e https://quiltdata.com
  -u USERNAME
  -n "ENCODE data"
  -d "#A549 #histone peak data #hg19"
  -f downloads/wgEncodeBroadHistoneNhaH3k36me3StdPk.broadPeak

• ENCDOE broadPeak format

• ENCODE Project

Notes

• For all REST calls, the content-type is application/JSON.
• Description fields automatically linkify URLs and support <a>, <i>, <em>, <strong>, <b> tags

POST /tables/

{
  'name': string,
  'description': text `<a>, <i>, <em>, <strong>, <b>` tags supported; automatic linkification of URLs
  'columns': [
    {
      'name': string,
      'sqlname': optional string,
      'description': optional text,
      'type' : one of 'String', 'Number', 'Image', 'Text'
    },
    ...
  ]
}

Table data as JSON object, includes id field with the table's identifier.

POST /tables/TABLE_ID/columns/

{
   'name': string,
   'sqlname': optional string,
   'description': text,
   'type': one of 'String', 'Number', 'Image', or 'Text'
}

Column data as JSON object, includes id field with the column's identifier.

DELETE /tables/TABLE_ID

PATCH /tables/TABLE_ID

{
   'name': string,
   'description': text
}

• Use column sqlname as keys in input data

POST /data/TABLE_ID/rows/

[
  {columnSqlname0: value0, columnSqlname1 : value1, ... },
  ...
]

GET /data/TABLE_ID/rows

• Rows are keyed by the Quilt Row ID field qrid
• NOTE: Currently limited to the first 500 rows

Row data as JSON object, keyed by column.sqlname.

GET /data/TABLE_ID/rows/ROW_ID

Row data as JSON object, keyed by column.sqlname.

POST /quilts/

{
  'left_table_id': int,
  'right_table_id': int,
  'left_column_id': int,
  'right_column_id': int,
  'jointype': one of 'inner', 'leftOuter', 'firstMatch'
}

Quilt info as JSON object, includes sqlname field with the quilt's identifier.

DELETE /quilts/QUILT_SQLNAME

• Performs a gene math operation on two tables
• Creates a new table with the result.
• Columns are specified by column.id.

POST /genemath/

{
  'operator': one of 'Intersect' or 'Subtract',
  'left_chr': integer (column id),
  'left_start': integer (column id),
  'left_end':  integer (column id),
  'right_chr':  integer (column id),
  'right_start': integer (column id),
  'right_end':  integer (column id)
}

JSON object representing the result table.