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motif2.py
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motif2.py
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# import modules
import re
import sys
import regex
from collections import defaultdict
#read file and get fasta lines
File=open(sys.argv[1], 'r').read().splitlines()
#### Get All motifs with exact match
print("-------------------------All motifs with exact match :--------------------")
def motifWithExactMatch():
### List of regular expressions.
L=['W[KRH]..[ALYFIMVW][DE]']
for line in File:
dic = defaultdict(list)
if line[0]=='>':
print (line)
if line[0]!='>':
count = 0
indexPositions = []
listOfMatchObs = []
### Get motifs on line for each regular expression into the list.
for l in L:
regexPattern = re.compile(l)
mainStr=line
iteratorOfMatchObs = regexPattern.finditer(mainStr)
### Get list of motifs and their count on line.
for matchObj in iteratorOfMatchObs:
indexPositions.append(matchObj.start())
listOfMatchObs.append(matchObj.group())
count = count + 1
### Print outputs.
for i in range(len(listOfMatchObs)):
dic[listOfMatchObs[i]].append(str(indexPositions[i]))
for i in dic:
print(i," ".join(dic[i]))
print("Count of found motifs on line:", count)
#### Function call.
motifWithExactMatch()
#### Get All motifs with five residues match
print("-------------------------All motifs with five residues match :--------------------")
def motifWithFiveResiduesMatch():
### List of regular expressions.
L=['W[KRH]..[ALYFIMVW]','[KRH]..[ALYFIMVW][DE]']
for line in File:
dic = defaultdict(list)
if line[0]=='>':
print (line)
if line[0]!='>':
count = 0
indexPositions = []
listOfMatchObs = []
### Get motifs on line for each regular expression into the list.
for l in L:
regexPattern = re.compile(l)
mainStr=line
iteratorOfMatchObs = regexPattern.finditer(mainStr)
### Get list of motifs and their count on line.
for matchObj in iteratorOfMatchObs:
indexPositions.append(matchObj.start())
listOfMatchObs.append(matchObj.group())
count = count + 1
### Print outputs.
for i in range(len(listOfMatchObs)):
dic[listOfMatchObs[i]].append(str(indexPositions[i]))
for i in dic:
print(i," ".join(dic[i]))
print("Count of found motifs on line:", count)
#### Function call.
motifWithFiveResiduesMatch()
#### Get All motifs with four residues match
print("-------------------------All motifs with four residues match :--------------------")
def motifWithFourResiduesMatch():
### List of regular expressions.
L=['W[KRH]..','..[ALYFIMVW][DE]','[KRH]..[ALYFIMVW]']
for line in File:
dic = defaultdict(list)
if line[0]=='>':
print (line)
if line[0]!='>':
count = 0
indexPositions = []
listOfMatchObs = []
### Get motifs on line for each regular expression into the list.
for l in L:
regexPattern = re.compile(l)
mainStr=line
iteratorOfMatchObs = regexPattern.finditer(mainStr)
### Get list of motifs and their count on line.
for matchObj in iteratorOfMatchObs:
indexPositions.append(matchObj.start())
listOfMatchObs.append(matchObj.group())
count = count + 1
### Print outputs.
for i in range(len(listOfMatchObs)):
dic[listOfMatchObs[i]].append(str(indexPositions[i]))
for i in dic:
print(i," ".join(dic[i]))
print("Count of found motifs on line:", count)
#### Function call.
motifWithFourResiduesMatch()