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#!/usr/bin/env python
# Usage: <inFile_1> <inFile_2> "/"
# Description: Separates paired end Illumina sequences into pairs
# and singlets. Also checks if the output sequences
# are in the same order in the resulting output files.
# Input: Two files with sequences in fastq format (inFile_1 and inFile_2).
# Output: 'outpair1.fastq' and 'outpair2.fastq' contains the
# sequence pairs. Sequences in 'outpair1.fastq' originates
# from the first imput file, and 'outpair2.fastq' from
# the other. 'outSingles1.fastq' and 'outSingles2.fastq'
# contains the singglet sequences from each input file.
# Citation: If you use this version of the program, please cite;
# Mats T"opel (2013) Open Laboratory Notebook.
# Copyright (C) 2013 Mats Topel.
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# GNU General Public License for more details.
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <>.
# TODO: Make sure that output is written to PWD.
import sys
import gc
#import io
from itertools import izip
# Identify the input files
f1 = sys.argv[1]
f2 = sys.argv[2]
# Identify the sequence ID's
def getSeqId():
with open(f1, 'r') as f:
first_line = f.readline()
return first_line[0:3]
seqID = getSeqId()
delim = sys.argv[3].strip('"\'') # Perhaps redundant to try to remove " and ' characters.
delim = ' '
# pairF1 = "%s.pair_1.fastq.txt" % f1 # Redundant.
# pairF2 = "%s.pair_2.fastq.txt" % f2 # Redundant.
class sequence(object):
def __init__(self):
self.Id = None
self.seq = None
self.qid = None
self.qual = None
def setId(self, line):
self.Id = line
def setSeq(self, line):
self.seq = line
def setQid(self, line):
self.qid = line
def setQual(self, line):
self.qual = line
def getId(self):
return self.Id
def getPairId(self):
return self.Id.split(delim)[0]
def getSeq(self):
return self.seq
def getQid(self):
return self.qid
def getQual(self):
return self.qual
def __str__(self):
return "%s%s%s%s" % (self.Id, self.seq, self.qid, self.qual)
class fastqFile(file):
def __init__(self, name, mode):
file.__init__(self, name, mode)
def readParts(self, partSize=256):
while True:
data =
if not data:
yield data
def Ids2Dict(self):
# Reads the file, one sequence object at the time, and identifies
# the sequence identifiers. The identifiers
# are then split at the indicated delimiter, and the first
# part is stored in a dictionary.
seqIdDict = {}
for seq in self.getSeqs():
seqIdDict[seq.getId().split(delim)[0]] = False
return seqIdDict
def cmpIds2Dict(self, fwDict, outPair, outSing, fileNr):
# Compair the sequence id's in the second file to the
# once in file 1 (stored in a dictionary). Then write
# sequence information to output files.
pair = False
if fileNr == 1:
pair = True
for seq in self.getSeqs():
seqId = seq.getId().split(delim)[0]
if fwDict[seqId] == pair:
# Set output file to be the "pairs" file.
out = outPair
# Set seqId in dict to "True" to indicate
# that a pair has been found.
fwDict[seqId] = True
# Set output file to the "singlets" file.
out = outSing
except KeyError:
# Insert a key from the second file in the
# dictionary if it's not allready there.
fwDict[seqId] = False
out = outSing
def getSeqs(self):
with self as f:
for line in f:
# if line[0:3] == getSeqId():
if line[0:3] == seqID:
# Create a sequence object.
seq = sequence()
elif seq.getId() != None and seq.getSeq() == None:
elif seq.getId() != None and seq.getSeq() != None and seq.getQid() == None:
elif seq.getId() != None and seq.getSeq() != None and seq.getQid() != None and seq.getQual() == None:
yield seq
def compSeqOrder(outPair_1, outPair_2):
count = 0
with outPair_1 as f1:
with outPair_2 as f2:
for (fwSeq, rwSeq) in izip(f1.getSeqs(), f2.getSeqs()):
if fwSeq.getPairId() == rwSeq.getPairId():
count += 1
return count
def noFileExt(fileName):
if fileName[-6:].lower() == ".fastq":
name = fileName[:-6]
ext = fileName[-6:]
return name, ext
def genFileName(inFile, outType):
name = noFileExt(inFile)[0]
ext = noFileExt(inFile)[1]
newName = name + outType + ext
return newName
#def getSeqId():
# with open(f1, 'r') as f:
# first_line = f.readline()
# return first_line[0:3]
def main():
# Generate fastqFile objects to read from and write to.
inFile1 = fastqFile(f1, 'r') # First sequence file to read from
inFile2 = fastqFile(f2, 'r') # Second sequence file to read from
outPair_1 = fastqFile(genFileName(f1, ".Pair"), 'w')
outPair_2 = fastqFile(genFileName(f2, ".Pair"), 'w')
outSing_1 = fastqFile(genFileName(f1, ".Singles"), 'w')
outSing_2 = fastqFile(genFileName(f2, ".Singles"), 'w')
# Create dictionary containing sequence id's from first file (info. on direction removed).
print "[--] Building initial dictionary of sequence id's in first file."
fwDict = inFile1.Ids2Dict()
# Release memory if possible
print "[--] Attempting memory garbage collection"
# Compair Id's in file 2 to the once in the dictionary, then write to outfiles.
print "[--] Comparing id's in second file to the dictionary."
inFile2.cmpIds2Dict(fwDict, outPair_2, outSing_2, 2)
# Compair Id's in file 1 to the once in the dictionary, then write to outfiles.
print "[--] Comparing id's in first file to the dictionary"
inFile1 = fastqFile(f1, 'r') # Open the first file again
inFile1.cmpIds2Dict(fwDict, outPair_1, outSing_1, 1)
# Check if sequences in the "pair" files are in the same order
outPair_1 = fastqFile(genFileName(f1, ".Pair"), 'r') # Change name of file later
outPair_2 = fastqFile(genFileName(f2, ".Pair"), 'r') # Change name of file later
print "[--] Check if sequences in 'pair' files are in the same order"
print "[op] %s sequnce pairs are in order" % compSeqOrder(outPair_1, outPair_2)
if __name__ == "__main__":