fasta_to_fastq.py

10/12/2014 14:12

Ce script python permet de générer un fichier fastq à partir d'un fichier fasta et un fichier contenant les valeurs de qualité des séquences fasta.

 

#!/usr/bin/env python
import sys
from Bio import SeqIO
from Bio.SeqIO.QualityIO import PairedFastaQualIterator

#Takes a FASTA file, which must have a corresponding .qual file,
# and makes a single FASTQ file.

if len(sys.argv) == 1:
        print "Please specify a  single FASTA file to convert."
        sys.exit()

filetoload = sys.argv[1]
basename = filetoload

#Chop the extension to get names for output files
if basename.find(".") != -1:
        basename = '.'.join(basename.split(".")[:-1])

try:
    fastafile = open(filetoload)
    qualfile = open(basename + ".qual")
except IOError:
    print "Either the file cannot be opened or there is no corresponding"
    print "quality file (" + basename +".qual)"
    sys.exit()

rec_iter = PairedFastaQualIterator(fastafile,qualfile)

SeqIO.write(rec_iter, open(basename + ".fastq", "w"), "fastq")
 

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