Mercurial > repos > tyty > structurefold
changeset 57:31d688722e7a draft
Uploaded
| author | tyty |
|---|---|
| date | Tue, 18 Nov 2014 01:01:21 -0500 |
| parents | 9d26c2e4953e |
| children | 971ef91f6b68 |
| files | get_reads/get_read.py get_reads/get_read.xml get_reads/map_info.txt get_reads/read_file.py get_reads/read_file.pyc get_reads/test.bam |
| diffstat | 6 files changed, 194224 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/get_reads/get_read.py Tue Nov 18 01:01:21 2014 -0500 @@ -0,0 +1,91 @@ +#!/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 * +import random +import string + +fasta_file = sys.argv[1] +map_file = sys.argv[2] +result_file = sys.argv[3] + +ospath = os.path.realpath(sys.argv[0]) +ost = ospath.split('/') +syspath = "" +for i in range(len(ost)-1): + syspath = syspath+ost[i].strip() + syspath = syspath+'/' + +rs = ''.join(random.sample(string.ascii_letters + string.digits, 8)) +os.system("mkdir "+syspath+"output_"+rs) + +syspathrs = syspath+"output_"+rs+'/' + +os.system("samtools view -F 0xfff "+map_file+"|cut -f 3,4 > "+syspathrs+"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(syspathrs+"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') + +os.system("rm -r "+syspathrs) + + + +f.close(); +h.close() + + + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/get_reads/get_read.xml Tue Nov 18 01:01:21 2014 -0500 @@ -0,0 +1,44 @@ +<tool id="get_read_pipeline" name="Get RT Stop Counts" version="1.0"> + <description></description> + <command interpreter="python">get_read.py $lib_file $map_file $output </command> + <requirements> + <requirement type="package" version="1.61">biopython</requirement> + <requirement type="package" version="1.7.1">numpy</requirement> + <requirement type="package" version="0.1.18">samtools</requirement> + </requirements> + <inputs> + <param name="lib_file" type="data" format="fasta" label="Reference genome/transcriptome"/> + <param name="map_file" type="data" format="bam" label="Mapped file"/> + </inputs> + <outputs> + <data name="output" format="txt"/> + </outputs> + <tests> + <test> + <param name="lib_file" value="test.bam" /> + <param name="map_file" value="com_rna.txt" /> + <output name="output" file="get_RT_stop_test.out" /> + </test> + </tests> + <help> + + +**TIPS**: + +----- + +**Input** + +* 1. A mapped (bam) file from Bowtie (or any other mapping program) +* 2. Reference library sequences (fasta) used to map the reads to + +----- + +**Output**: + +A text file with reverse transcription stop counts mapped to each nucleotide (RTSC file) + + + + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/get_reads/map_info.txt Tue Nov 18 01:01:21 2014 -0500 @@ -0,0 +1,194068 @@ +25s 1551 +AT5G08080.2 483 +AT5G08080.1 483 +AT5G08080.3 516 +AT5G34833.1 44 +AT3G25950.1 1052 +AT2G25250.1 11 +AT5G29040.1 2556 +25s 1310 +AT4G24100.1 33 +25s 719 +AT3G58865.1 849 +AT3G07850.1 40 +AT4G06499.1 1270 +gi|20197903:2706-4513 722 +AT4G02710.1 82 +25s 1310 +AT1G73230.1 40 +AT3G12110.1 967 +AT3G18780.1 1077 +AT3G18780.2 1106 +25s 1310 +AT1G73230.1 40 +25s 1310 +AT2G23090.1 64 +AT1G12040.1 1586 +AT1G26250.1 679 +AT1G12040.1 1445 +AT1G12040.1 1532 +AT2G37170.1 328 +AT2G37180.1 333 +AT4G09432.1 252 +AT3G26020.2 1882 +AT3G26020.3 1944 +AT3G26020.1 1938 +AT3G26020.4 1995 +ATMG01390.1 384 +AT3G09260.1 9 +25s 1551 +25s 1310 +AT5G50020.2 252 +AT5G50020.1 361 +25s 1310 +AT3G04670.2 71 +AT3G04670.1 8 +25s 1310 +AT4G15545.1 915 +gi|20197903:2706-4513 714 +AT1G55675.1 29 +25s 1567 +AT5G47800.1 110 +AT2G08986.1 556 +AT1G40104.1 856 +25s 1310 +AT3G04670.2 71 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/get_reads/read_file.py Tue Nov 18 01:01:21 2014 -0500 @@ -0,0 +1,21 @@ +#!/usr/bin/env python +# -*- coding: utf-8 -*- + +import sys + + + +def read_t_file(in_file): + f = open(in_file); + result = []; + for aline in f.readlines(): + temp = []; + tline = aline.strip(); + tl = tline.split('\t'); + for i in range(0, len(tl)): + temp.append(tl[i].strip()); + result.append(temp); + f.close(); + return result; + +