Mercurial > repos > gpovysil > range2tag
changeset 0:0b486eaca66e draft
planemo upload for repository https://github.com/gpovysil/galaxy/tools/range2tag commit 16b1092dfe1052f9560188e67f39009f1e4b32bc
| author | gpovysil |
|---|---|
| date | Wed, 16 May 2018 04:53:11 -0400 |
| parents | |
| children | 24d6b738df6e |
| files | range2tag.py range2tag.xml ranges.txt |
| diffstat | 3 files changed, 185 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/range2tag.py Wed May 16 04:53:11 2018 -0400 @@ -0,0 +1,125 @@ +"""range2tag.py + +Author -- Gundula Povysil +Contact -- povysil@bioinf.jku.at + +Takes a SAM file, start and stop positions as input and prints all tags +of reads that overlap with regions to user specified output file. +======= ========== ================= ================================ +Version Date Author Description +0.0.2 2018-05-15 Gundula Povysil - +======= ========== ================= ================================ + +USAGE: python range2tag.py inputFile.sam ranges.txt outputFile.txt +""" + + +import numpy as np +import re +import argparse +import sys +import os + +def make_argparser(): + parser = argparse.ArgumentParser(description='Takes a SAM file, start and stop positions as input and prints all tags of reads that overlap with regions to user specified output file.') + parser.add_argument('inputFile', + help='SAM file with aligned reads.') + parser.add_argument('rangesFile', + help='TXT file with start and stop positions.') + parser.add_argument('outputFile', + help='Output TXT file with tags that are within specified regions.') + return parser + +def range2tag(argv): + parser = make_argparser() + args=parser.parse_args(argv[1:]) + + inputFile = args.inputFile + rangesFile = args.rangesFile + outputFile = args.outputFile + + if os.path.isfile(inputFile) is False: + print("Error: Could not find '{}'".format(inputFile)) + exit(0) + + if os.path.isfile(rangesFile) is False: + print("Error: Could not find '{}'".format(rangesFile)) + exit(0) + + with open(rangesFile, 'r') as regs: + range_array = np.genfromtxt(regs, skip_header=0, delimiter='\t', comments='#') + + start_posList = range_array[:,0].astype(int) + stop_posList = range_array[:,1].astype(int) + + print(start_posList) + print(stop_posList) + + if len(start_posList) == 0: + print("Error: start_positions is empty") + exit(2) + + if len(stop_posList) == 0: + print("Error: end_positions is empty") + exit(3) + + if len(start_posList) != len(stop_posList): + print("start_positions and end_positions do not have the same length") + exit(3) + + with open(inputFile, 'r') as sam: + data_array = np.genfromtxt(sam, skip_header=0, delimiter='\t', usecols=range(11), comments='#', dtype='string') + + tags = np.array(data_array[:, 0]) + ref_pos = np.array(data_array[:, 3]).astype(int) + cigar = np.array(data_array[:, 5]) + + lst = [] + ind = [] + start_posList = np.array(start_posList).astype(int) + stop_posList = np.array(stop_posList).astype(int) + + for start_pos, stop_pos in zip(start_posList, stop_posList): + start_pos = start_pos - 3 + stop_pos = stop_pos + 3 + mut_tags = None + for t in range(0, len(tags)): + c_split = re.split('([A-Z])', cigar[t]) + cigar_long = None + + for i in range(1, len(c_split), 2): + if cigar_long is None: + cigar_long = np.repeat(c_split[i], c_split[i - 1]) + else: + cigar_long = np.concatenate((cigar_long, np.repeat(c_split[i], c_split[i - 1])), axis=0) + + pos = ref_pos[t] + seq_pos = 0 + # print(pos) + if pos < stop_pos: + for j in range(0, len(cigar_long)): + if pos >= stop_pos: + break + if cigar_long[j] in ("M", "D", "N"): + pos += 1 + # print(pos) + if pos > start_pos: + if mut_tags is None: + mut_tags = np.array((tags[t])) + else: + mut_tags = np.vstack((mut_tags, np.array(tags[t]))) + + index = np.repeat("{}_{}".format(start_pos, stop_pos), len(mut_tags)) + ind.append(index) + lst.append(mut_tags) + + index = np.concatenate((ind)) + tags = np.concatenate((lst)) + mut_tags = np.column_stack((index, tags)) + + np.savetxt(outputFile, mut_tags, fmt="%s") + print("File saved under {} in {}!".format(outputFile, os.getcwd())) + + +if __name__ == '__main__': + sys.exit(range2tag(sys.argv))
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/range2tag.xml Wed May 16 04:53:11 2018 -0400 @@ -0,0 +1,54 @@ +<?xml version="1.0" encoding="UTF-8"?> +<tool id="range2tag" name="Duplex Sequencing Analysis: range2tag" version="0.0.1"> + <requirements> + <requirement type="package" version="2.7">python</requirement> + </requirements> + <description>Tool that extracts tags of reads that are within user-specified regions</description> + <command> + python2 $__tool_directory__/range2tag.py "$file1" "$file2" "$output" + </command> + <inputs> + <param name="file1" type="data" format="sam" label="Dataset 1: SAM file with aligned reads." optional="false" help="SAM File with reads aligned to reference."/> + <param name="file2" type="data" format="txt" label="Dataset 2: TXT file with start and stop positions of regions." optional="false" help="Tab delimited TXT file with start and stop positions of regions."/> + </inputs> + <outputs> + <data name="output" format="tabular" /> + </outputs> + <help> <![CDATA[ +**What it does** + + This tool takes a SAM file and a TXT file with start and stop positions as input and prints all tags of reads that overlap with regions to user specified output file. + + +**Input** + + **Dataset 1:** SAM file of aligned reads. + + **Dataset 2:** Tab delimited TXT file with start and stop positions. + +**Output** + + The output is a tabular file of tags of all reads that overlap the user-specified regions with start_stop in the first column and the tag in the second column. + + +**About Author** + + Author: Gundula Povysil, MD, PhD + + Department: Institute of Bioinformatics, Johannes Kepler University Linz, Austria + + Contact: gpovysil@gmail.com + + ]]> + + </help> + <citations> + <citation type="bibtex"> + @misc{duplex, + author = {Heinzl, Monika}, + year = {2018}, + title = {Development of algorithms for the analysis of duplex sequencing data} + } + </citation> + </citations> +</tool> \ No newline at end of file