Mercurial > repos > tyty > structurefold
diff get_reads/get_read.py @ 2:297cdb01d656 draft
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author | tyty |
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date | Mon, 15 Sep 2014 14:47:42 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/get_reads/get_read.py Mon Sep 15 14:47:42 2014 -0400 @@ -0,0 +1,77 @@ +#!/usr/bin/env python +# -*- coding: utf-8 -*- + +import sys +#from galaxy.tools.read_file import * +from Bio import SeqIO +import os +from read_file import * + +fasta_file = sys.argv[1] +map_file = sys.argv[2] +result_file = sys.argv[3] + +os.system("samtools view -F 0xfff "+map_file+"|cut -f 3,4 > map_info.txt") + +fasta_sequences = SeqIO.parse(open(fasta_file),'fasta'); +length_seq = {}; +for seq in fasta_sequences: + nuc = seq.id; + length_seq[nuc] = len(seq.seq.tostring()); + + + +mapping = {} +transcripts = [] + +f = open("map_info.txt"); +for aline in f.readlines(): + tline = aline.strip(); + tl = tline.split('\t'); + if tl[0].strip() not in transcripts: + transcripts.append(tl[0].strip()); + mapping[tl[0].strip()] = []; + + mapping[tl[0].strip()].append(tl[1].strip()); + +distribution = {}; +coverage = {}; +for transcript in length_seq: + distribution[transcript] = []; + for i in range(0, length_seq[transcript]): + distribution[transcript].append(0); + sum_count = float(0); + if transcript in mapping: + for j in range(0, len(mapping[transcript])): + index = mapping[transcript][j]; + #count = reads[mapping[transcript][j][0]]; + sum_count = sum_count + 1; + distribution[transcript][int(index)-1] = distribution[transcript][int(index)-1] + 1; + coverage[transcript] = float(sum_count)/float(length_seq[transcript]); + else: + coverage[transcript] = 0 + + + + + +h = file(result_file, 'w') +for transcript in length_seq: + h.write(transcript); + h.write('\n') + for i in range(0, length_seq[transcript]): + h.write(str(distribution[transcript][i])) + h.write('\t') + h.write('\n') + h.write('\n') + + + + + +f.close(); +h.close() + + + +