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#!/usr/bin/env python
# Copyright (c) 2016, The Regents of the University of California.
import sys
import os
class fastaModel(object):
"""
Contains methods for writing data to a file in the fasta format
"""
def __init__(self, fileHandle):
self.fileHandle = fileHandle
self.currSeq = ""
def writeName(self, name):
"""
Writes the given name to the fileHandle in the fasta format
"""
self.fileHandle.write(">%s " % name.strip())
def writeDescription(self, description):
"""
Writes the given description and the stored sequence to the file
"""
self.fileHandle.write("%s\n%s\n" % (description.strip(), self.currSeq))
def writeSequence(self, sequence):
"""
Stores the given sequence until a call to writeDescription is made
so that the description and sequence will be stored in the correct
fasta order
"""
self.currSeq = sequence.strip()
def convertFastqToFasta(inputFilename, outputFilename):
"""
Converts the given fastq file (inputFilename) to an equilivalent fasta file
(outputFilename). The fastq's quality information is converted to a fasta's
'description' field. Sequence and name fields are left alone
"""
inputFile = open(inputFilename, "rb")
outputFile = open(outputFilename, "wb")
model = fastaModel(outputFile)
for line in inputFile:
if line.startswith("@"): # Line is a name
model.writeName(line[1:])
elif line.startswith('+'): # Next line is the quality
quality = inputFile.next()
model.writeDescription(quality)
else: # Line is the sequence
model.writeSequence(line)
outputFile.close()
if __name__ == '__main__':
if len(sys.argv) != 3:
print "Usage: <input filename> <output filename>"
exit(1)
inputFilename = sys.argv[1]
outputFilename = sys.argv[2]
if not os.path.isfile(inputFilename):
print "Error: %s doesn't exist" % inputFilename
exit(2)
convertFastqToFasta(inputFilename, outputFilename)
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