Mercurial > repos > tyty > structurefold
view Iterative_mapping/truncate.py @ 93:f1eb39775b93 draft
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author | tyty |
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date | Mon, 16 Feb 2015 02:29:27 -0500 |
parents | 9d26c2e4953e |
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#!/usr/bin/env python # -*- coding: utf-8 -*- import sys from Bio import SeqIO fasta_file = sys.argv[1] shift_in = sys.argv[2] result_file = sys.argv[3] length = sys.argv[4] t_end = sys.argv[5] shift = int(shift_in) fasta_sequences = SeqIO.parse(open(fasta_file),'fasta'); h = file(result_file,'w') for seq in fasta_sequences: nuc = seq.id; sequence = seq.seq.tostring(); if (len(sequence)-shift)>=int(length): h.write('>'+nuc) h.write('\n') if t_end == 'three_end': h.write(sequence[0:(len(sequence)-shift)]) if t_end == 'five_end': h.write(sequence[(shift):(len(sequence))]) h.write('\n') h.close()