Mercurial > repos > iuc > ivar_trim
changeset 4:db536ad45f28 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 693df287d23b0fd9dfd134b41d401a438c3f5ad6"
| author | iuc |
|---|---|
| date | Mon, 22 Jun 2020 07:30:46 -0400 |
| parents | 5d6ed46cc101 |
| children | cf65217ad61c |
| files | completemask.py ivar_trim.xml sanitize_bed.py test-data/covid19/ARTIC-V1-bad.bed |
| diffstat | 4 files changed, 262 insertions(+), 5 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/completemask.py Mon Jun 22 07:30:46 2020 -0400 @@ -0,0 +1,28 @@ +#!/usr/bin/env python + +import sys + + +if __name__ == '__main__': + with open(sys.argv[1]) as i: + getmasked_output = i.readline().strip() + + if not getmasked_output: + print() + print('No affected primer binding sites found!') + else: + masked_primers = getmasked_output.split('\t') + with open(sys.argv[2]) as i: + amplicon_data = [line.strip().split('\t') for line in i] + + masked_complete = [] + for primer in masked_primers: + for amplicon in amplicon_data: + if primer in amplicon: + masked_complete += amplicon + result = '\t'.join(sorted(set(masked_complete))) + print() + print('Removing reads primed with any of:') + print(result) + with open(sys.argv[1], 'w') as o: + o.write(result + '\n')
--- a/ivar_trim.xml Fri Jun 05 04:12:52 2020 -0400 +++ b/ivar_trim.xml Mon Jun 22 07:30:46 2020 -0400 @@ -1,17 +1,23 @@ -<tool id="ivar_trim" name="ivar trim" version="@VERSION@+galaxy0"> +<tool id="ivar_trim" name="ivar trim" version="@VERSION@+galaxy1"> <description>Trim reads in aligned BAM</description> <macros> <import>macros.xml</import> </macros> - <expand macro="requirements" /> + <expand macro="requirements"> + <requirement type="package" version="3.8.1">python</requirement> + </expand> <expand macro="version_command" /> <command detect_errors="exit_code"><![CDATA[ #if $primer.source == "history" - ln -s '$primer.input_bed' bed.bed && + cp '$primer.input_bed' bed.bed && #else - ln -s '$primer.cached_bed.fields.path' bed.bed && - #end if + cp '$primer.cached_bed.fields.path' bed.bed && + #end if + python '$__tool_directory__/sanitize_bed.py' bed.bed && + ln -s '$input_bam' sorted.bam && + ln -s '${input_bam.metadata.bam_index}' sorted.bam.bai && + ivar trim -i sorted.bam -b bed.bed @@ -57,6 +63,13 @@ <param name="inc_primers" value="true" /> <output name="output_bam" file="covid19/PC00101P_sub.sorted.bam" compare="sim_size" delta="300000"/> </test> + <test> + <!-- Test with primer bed file that needs to be sanitized --> + <param name="input_bam" value="covid19/PC00101P_sub.sorted.bam" /> + <param name="input_bed" value="covid19/ARTIC-V1-bad.bed" /> + <param name="inc_primers" value="true" /> + <output name="output_bam" file="covid19/PC00101P_sub.sorted.bam" compare="sim_size" delta="300000"/> + </test> <!-- #1: Zika data--> <test> <conditional name="primer">
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sanitize_bed.py Mon Jun 22 07:30:46 2020 -0400 @@ -0,0 +1,20 @@ +#!/usr/bin/env python + +import sys + + +with open(sys.argv[1]) as i: + bed_data = i.readlines() + +sanitized_data = [] +try: + for record in bed_data: + fields = record.split('\t') + sanitized_data.append( + '\t'.join(fields[:4] + ['60'] + fields[5:]) + ) +except IndexError: + pass # leave column number issue to getmasked +else: + with open(sys.argv[1], 'w') as o: + o.writelines(sanitized_data)
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