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NWalign.py
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executable file
·297 lines (272 loc) · 12 KB
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#!/usr/bin/env python
# Needleman-Wunsch dynamic programming for pairwise protein sequence alignment
# Copyright 2015 Chengxin Zhang @ Yang Zhang lab
# Inspired by NWAlign.java by Ren-Xiang Yan and NWalign.f by Yang Zhang
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later version.
docstring='''
Pairwise sequence alignment by standard Needleman-Wunsch algorithm
NWalign F1.fasta F2.fasta (align two sequences in fasta file)
NWalign F1.pdb F2.pdb 1 (align two sequences in PDB file)
NWalign F1.fasta F2.pdb 2 (align Sequence 1 in fasta and 2 in pdb)
NWalign GKDGL EVADELVSE 3 (align two sequences typed by keyboard)
NWalign GKDGL F.fasta 4 (align Sequence 1 by keyboard and 2 in fasta)
NWalign GKDGL F.pdb 5 (align Sequence 1 by keyboard and 2 in pdb)
'''
import sys
gap_open=-11 # gap gapopen
gap_extn=-1 # gap gapext
Blosum62Matrix=[
# A R N D C Q E G H I L K M F P S T W Y V B Z X *
[ 4,-1,-2,-2 ,0,-1,-1 ,0,-2,-1,-1,-1,-1,-2,-1 ,1 ,0,-3,-2 ,0,-2,-1 ,0,-4],#A
[-1 ,5 ,0,-2,-3 ,1 ,0,-2 ,0,-3,-2 ,2,-1,-3,-2,-1,-1,-3,-2,-3,-1 ,0,-1,-4],#R
[-2 ,0 ,6 ,1,-3 ,0 ,0 ,0 ,1,-3,-3 ,0,-2,-3,-2 ,1 ,0,-4,-2,-3 ,3 ,0,-1,-4],#N
[-2,-2 ,1 ,6,-3 ,0 ,2,-1,-1,-3,-4,-1,-3,-3,-1 ,0,-1,-4,-3,-3 ,4 ,1,-1,-4],#D
[ 0,-3,-3,-3 ,9,-3,-4,-3,-3,-1,-1,-3,-1,-2,-3,-1,-1,-2,-2,-1,-3,-3,-2,-4],#C
[-1 ,1 ,0 ,0,-3 ,5 ,2,-2 ,0,-3,-2 ,1 ,0,-3,-1 ,0,-1,-2,-1,-2 ,0 ,3,-1,-4],#Q
[-1 ,0 ,0 ,2,-4 ,2 ,5,-2 ,0,-3,-3 ,1,-2,-3,-1 ,0,-1,-3,-2,-2 ,1 ,4,-1,-4],#E
[ 0,-2 ,0,-1,-3,-2,-2 ,6,-2,-4,-4,-2,-3,-3,-2 ,0,-2,-2,-3,-3,-1,-2,-1,-4],#G
[-2 ,0 ,1,-1,-3 ,0 ,0,-2 ,8,-3,-3,-1,-2,-1,-2,-1,-2,-2 ,2,-3 ,0 ,0,-1,-4],#H
[-1,-3,-3,-3,-1,-3,-3,-4,-3 ,4 ,2,-3 ,1 ,0,-3,-2,-1,-3,-1 ,3,-3,-3,-1,-4],#I
[-1,-2,-3,-4,-1,-2,-3,-4,-3 ,2 ,4,-2 ,2 ,0,-3,-2,-1,-2,-1 ,1,-4,-3,-1,-4],#L
[-1 ,2 ,0,-1,-3 ,1 ,1,-2,-1,-3,-2 ,5,-1,-3,-1 ,0,-1,-3,-2,-2 ,0 ,1,-1,-4],#K
[-1,-1,-2,-3,-1 ,0,-2,-3,-2 ,1 ,2,-1 ,5 ,0,-2,-1,-1,-1,-1 ,1,-3,-1,-1,-4],#M
[-2,-3,-3,-3,-2,-3,-3,-3,-1 ,0 ,0,-3 ,0 ,6,-4,-2,-2 ,1 ,3,-1,-3,-3,-1,-4],#F
[-1,-2,-2,-1,-3,-1,-1,-2,-2,-3,-3,-1,-2,-4 ,7,-1,-1,-4,-3,-2,-2,-1,-2,-4],#P
[ 1,-1 ,1 ,0,-1 ,0 ,0 ,0,-1,-2,-2 ,0,-1,-2,-1 ,4 ,1,-3,-2,-2 ,0 ,0 ,0,-4],#S
[ 0,-1 ,0,-1,-1,-1,-1,-2,-2,-1,-1,-1,-1,-2,-1 ,1 ,5,-2,-2 ,0,-1,-1 ,0,-4],#T
[-3,-3,-4,-4,-2,-2,-3,-2,-2,-3,-2,-3,-1 ,1,-4,-3,-2,11 ,2,-3,-4,-3,-2,-4],#W
[-2,-2,-2,-3,-2,-1,-2,-3 ,2,-1,-1,-2,-1 ,3,-3,-2,-2 ,2 ,7,-1,-3,-2,-1,-4],#Y
[ 0,-3,-3,-3,-1,-2,-2,-3,-3 ,3 ,1,-2 ,1,-1,-2,-2 ,0,-3,-1 ,4,-3,-2,-1,-4],#V
[-2,-1 ,3 ,4,-3 ,0 ,1,-1 ,0,-3,-4 ,0,-3,-3,-2 ,0,-1,-4,-3,-3 ,4 ,1,-1,-4],#B
[-1 ,0 ,0 ,1,-3 ,3 ,4,-2 ,0,-3,-3 ,1,-1,-3,-1 ,0,-1,-3,-2,-2 ,1 ,4,-1,-4],#Z
[ 0,-1,-1,-1,-2,-1,-1,-1,-1,-1,-1,-1,-1,-1,-2 ,0 ,0,-2,-1,-1,-1,-1,-1,-4],#X
[-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4 ,1]]#*
seqW="ARNDCQEGHILKMFPSTWYVBZX*" # Amino acide order in scoring matrix
def readFastaOrRawSequence(infile="F1.fasta"):
'''read a sequence from a Fasta file or a text file.'''
br=open(infile,'rU').read()
seq=br.split('>')[1].splitlines()[1:] if '>' in br else br.splitlines()
return ''.join([line.strip() for line in seq])
def readPDB(infile="F1.pdb"):
'''read a sequence from a PDB file'''
from pdb2fasta import pdb2seq
header_list,sequence_list=pdb2seq(infile,
PERMISSIVE="MSE",outfmt="PDB",allowX=True)
return sequence_list[0]
def empty_matrix(N_rows, N_cols, fill=0):
'''Return a matrix (list of lists) which has `N_rows` rows and `N_cols`
columns. Each element of the matrix equals to `fill`'''
return [[fill for e in range(N_cols)]
for e in range(N_rows)]
def print_matrix(matrix=[[]],f1='',f2=''):
'''Print matrix in user friendly format. For debugging'''
f1='^'+f1 if f1 else '^'+' '*len(matrix)
f2=' ^'+f2
print '\t'.join(list(f2))
for i,row in enumerate(matrix):
print '\t'.join([f1[i]]+[str(e) for e in row])
def aa2int(f1="GKDGL"):
''' Convert AA sequence to interger according to the following mapping
A R N D C Q E G H I L K M F P S T W Y V B Z X *
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23
'''
return [[i for i in range(len(seqW)) if c==seqW[i]][0] for c in f1]
def print_alignment(sequenceA='',sequenceB=''):
'''print pairwise sequence alignment'''
sequenceM='' # identity string. colon for exact match.
L_ali=0
for i in range(len(sequenceA)):
if sequenceA[i]==sequenceB[i]:
sequenceM+=':'
else:
sequenceM+=' '
if sequenceA[i]!='-' and sequenceB[i]!='-':
L_ali+=1
len2=len(sequenceB.replace('-',''))
L_id=sequenceM.count(':')
identity=1.*L_id/len2 # Sequence identity
print "Aligned length: %u"%(L_ali)
print "Identical length: %u"%(L_id)
print "Sequence identity: %.3f (= %u/ %u)\n"%(identity,L_id,len2)
print sequenceA
print sequenceM
print sequenceB
print ''.join([str(i%10) for i in range(1,len(sequenceA)+1)])+'\n' #resi
def initialize_matrix(len1=0,len2=0,alternative=True):
'''initialize Dynamic Programming matrices
len1 - length of sequence 1
len2 - length of sequence 2
alternaive - whether to adopt alternative matrix initialization by wei zheng
'''
val=empty_matrix(len1+1,len2+1)
preV=empty_matrix(len1+1,len2+1) # penalty score of horizontal long gap
preH=empty_matrix(len1+1,len2+1) # penalty score of vertical long gap
jpV=empty_matrix(len1+1,len2+1)
jpH=empty_matrix(len1+1,len2+1)
idir=empty_matrix(len1+1,len2+1,fill='')
# fill first row/column of dynamic programming score matrix val,
# and path matrix idir
for i in range(1,len1+1):
idir[i][0]='-'
jpH[i][0]=i
for j in range(1,len2+1):
idir[0][j]='|'
jpV[0][j]=j
for i in range(1,len1+1):
val[i][0]=gap_open+gap_extn*(i-1)
for j in range(1,len2+1):
val[0][j]=gap_open+gap_extn*(j-1)
if alternative:
init_min=-999999999 # -1-sys.max
for i in range(1,len1+1):
preH[i][0]=gap_open+gap_extn*(i-1)
for j in range(1,len2+1):
preV[0][j]=gap_open+gap_extn*(j-1)
for i in range(len1+1):
preV[i][0]=init_min
for j in range(len2+1):
preH[0][j]=init_min
else:
for i in range(1,len1+1):
preV[i][0]=gap_open+gap_extn*(i-1)
for j in range(1,len2+1):
preH[0][j]=gap_open+gap_extn*(j-1)
return val,preV,preH,jpV,jpH,idir
def calcualte_score_gotoh(f1="GKDGL",f2="EVADELVSE", imut=Blosum62Matrix,
gap_open=gap_open, gap_extn=gap_extn): # "imut" is scoring matrix
'''Calculate the dynamic programming matrix using Gotoh algorithm.
Return these matrices: idir, jpV,jpH
idir - Path
\ : match-mismatch
- : horizontal gap (deletion)
| : vertical gap (insertion)
jpV - horizontal long gap number
jpH - vertical long gap number
All matrices are in the size of [len(f1)+1]*[len(f2)+1]
'''
# H, V, jpV, jpH are variable names taken from NWAlign.java,
# which in term derived from NWalign.f
# Since Fortran array indexing is column-wise, as oppose to row-wise
# array indexing in Python, the variable names do not actually reflect
# whether they are "horizontal" or "vertical" in this script
# initialize matrices
len1=len(f1)
len2=len(f2)
score=empty_matrix(len1+1,len2+1) # score of align i in f1 to j in f2
val,preV,preH,jpV,jpH,idir=initialize_matrix(len1,len2,alternative=True)
# convert char sequence to int sequence (aa2int)
seq1=[[i for i in range(len(seqW)) if c==seqW[i]][0] for c in f1]
seq2=[[i for i in range(len(seqW)) if c==seqW[i]][0] for c in f2]
# calculate score for local match-mismatch
for i in range(len1):
for j in range(len2):
score[i+1][j+1]=imut[seq1[i]][seq2[j]]
# fill val and idir
for i in range(1,len1+1):
for j in range(1,len2+1):
# penalty of consective deletion
preV[i][j]=max(val[i][j-1]+gap_open,preV[i][j-1]+gap_extn)
jpV[i][j]=jpV[i][j-1]+1 if preV[i][j]==preV[i][j-1]+gap_extn else 1
# penalty of consective insertion
preH[i][j]=max(val[i-1][j]+gap_open,preH[i-1][j]+gap_extn)
jpH[i][j]=jpH[i-1][j]+1 if preH[i][j]==preH[i-1][j]+gap_extn else 1
D=val[i-1][j-1]+score[i][j] # match-mismatch \
V=preV[i][j] # deletion -
H=preH[i][j] # insertion |
val[i][j]=max(D,V,H)
if val[i][j]==D:
idir[i][j]='\\'
if val[i][j]==V:
idir[i][j]+='-'
if val[i][j]==H:
idir[i][j]+='|'
return idir, jpV,jpH
def trace_back_gotoh(idir,jpV,jpH,f1="GKDGL",f2="EVADELVSE"):
'''trace back dynamic programming path to dicipher pairwise alignment
return a two-element list for the diciphered pairwise alignment'''
len1=len(f1)
len2=len(f2)
# re-fill first row/column of path matrix idir for back tracing
for i in range(1,len1+1):
idir[i][0]='|'
for j in range(1,len2+1):
idir[0][j]='-'
sequenceA=''
sequenceB=''
len1=len(f1)
len2=len(f2)
i=len1
j=len2
while(i+j):
gaplen=0
if 'none' in idir[i][j]:
pass
elif '-' in idir[i][j]:
gaplen=jpV[i][j]
sequenceA='-'*gaplen+sequenceA
sequenceB=f2[-gaplen:]+sequenceB
f2=f2[:-gaplen]
j=j-gaplen
elif '|' in idir[i][j]:
gaplen=jpH[i][j]
sequenceA=f1[-gaplen:]+sequenceA
sequenceB='-'*gaplen+sequenceB
f1=f1[:-gaplen]
i=i-gaplen
elif '\\' in idir[i][j]:
sequenceA=f1[-1]+sequenceA
sequenceB=f2[-1]+sequenceB
f1=f1[:-1]
f2=f2[:-1]
i=i-1
j=j-1
return sequenceA,sequenceB
def NeedlemanWunsch(f1="GKDGL",f2="EVADELVSE", imut=Blosum62Matrix,
gap_open=gap_open, gap_extn=gap_extn): # "imut" is scoring matrix
'''Needleman-Wunsch dynamic programming algorithm
GapPenalty=gap_open+gap_extn*(k-1), where k is gap number'''
f1=f1.upper().replace('-','').strip()
f2=f2.upper().replace('-','').strip()
# idir (DP path); jpV (Horizontal jump number); jpH (Vertical jump number)
idir,jpV,jpH=calcualte_score_gotoh(f1, f2, imut, gap_open, gap_extn)
# sequenceA (aligned f1); sequenceB (aligned f2)
sequenceA,sequenceB=trace_back_gotoh(idir,jpV,jpH,f1,f2)
print_alignment(sequenceA,sequenceB)
return sequenceA,sequenceB
if __name__=="__main__":
if len(sys.argv)<2:
sys.stderr.write(docstring)
exit()
elif len(sys.argv)<4:
input_mode='0'
else:
input_mode=sys.argv[3]
# parse input sequence
if input_mode=='0': # align two sequences in fasta file
f1=readFastaOrRawSequence(sys.argv[1])
f2=readFastaOrRawSequence(sys.argv[2])
elif input_mode=='1': # align two sequences in PDB file
f1=readPDB(sys.argv[1])
f2=readPDB(sys.argv[2])
elif input_mode=='2': # align Sequence 1 in fasta and 2 in pdb
f1=readFastaOrRawSequence(sys.argv[1])
f2=readPDB(sys.argv[2])
elif input_mode=='3': # align two sequences typed by keyboard
f1=sys.argv[1].strip()
f2=sys.argv[2].strip()
elif input_mode=='4': # align Sequence 1 by keyboard and 2 in fasta
f1=sys.argv[1].strip()
f2=readFastaOrRawSequence(sys.argv[2])
elif input_mode=='5': # align Sequence 1 by keyboard and 2 in fasta
f1=sys.argv[1].strip()
f2=readPDB(sys.argv[2])
else:
sys.stderr.write("ERROR! Unsupported file type "+input_mode+docstring)
exit()
print "\nLength of sequence 1:\t"+str(len(f1))+" ->"+sys.argv[1]
print "Length of sequence 2:\t"+str(len(f2))+" ->"+sys.argv[2]
NeedlemanWunsch(f1,f2)