fastxTranslate.py

#/usr/bin/env python

from Bio import SeqIO
import sys

def guessFileType(filename):
    if filename.endswith('fasta') or filename.endswith('fa'):
        fileType = 'fasta'
    elif filename.endswith('fastq') or filename.endswith('fq'):
        fileType = 'fastq'
    else:
        fileType = 'cannot regconize file type [fasta|fastq]'
    return fileType

def main(filename):
    fileType = guessFileType(filename)
    with open(filename,'ru') as seqfile:
        for record in SeqIO.parse(seqfile,fileType):
            startpos = record.seq.find('ATG')
            orf = record.seq[startpos:]
            if len(set(record.seq) -  {'A','T','C','G','N'}) != 0:
                sys.exit('Not DNA sequence')
            if len(orf) > 0:
                print '>%s\n%s'  %(record.id, orf.translate())
    return 0

if __name__ == '__main__':
    if len(sys.argv) != 2:
        sys.exit('usage: python %s <filename [fasta|fastq]>' %sys.argv[0])
    main( sys.argv[1])