Mercurial > repos > bgruening > glimmer3
view glimmer2seq.py @ 2:b1ad88bbc5fa draft default tip
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author | bgruening |
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date | Mon, 12 Aug 2013 11:55:07 -0400 |
parents | 841357e0acbf |
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#!/usr/bin/env python """ Input: DNA FASTA file + Glimmer ORF file Output: ORF sequences as FASTA file Author: Bjoern Gruening """ import sys, os from Bio import SeqIO from Bio.SeqRecord import SeqRecord def glimmer2seq( glimmer_prediction = sys.argv [1], genome_sequence = sys.argv[2], outfile = sys.argv[3] ): if len(sys.argv) >= 4: glimmerfile = open( glimmer_prediction, "r") sequence = open( genome_sequence ) else: print "Missing input values." sys.exit() fastafile = SeqIO.parse(sequence, "fasta") sequences = dict() seq_records = list() for entry in fastafile: sequences[entry.description] = entry for line in glimmerfile: if line.startswith('>'): entry = sequences[ line[1:].strip() ] else: orf_start = int(line[8:17]) orf_end = int(line[18:26]) orf_name = line[0:8] if orf_start <= orf_end: seq_records.append( SeqRecord( entry.seq[ orf_start-1 : orf_end ], id = orf_name, description = entry.description ) ) else: seq_records.append( SeqRecord( entry.seq[ orf_end-1 : orf_start ].reverse_complement(), id = orf_name, description = entry.description ) ) SeqIO.write( seq_records, outfile, "fasta" ) glimmerfile.close() sequence.close() if __name__ == "__main__" : glimmer2seq()