Mercurial > repos > dfornika > primer_scheme_to_amplicon_intervals

changeset 0:187f21b8e049 draft default tip

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"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/primer_scheme_to_amplicon_intervals commit a0982235f27e688a19733cfaaaf3ec2cfacb6312-dirty"
author dfornika
date Wed, 18 Mar 2020 03:00:48 +0000
parents
children
files primer_scheme_to_amplicon_intervals.py primer_scheme_to_amplicon_intervals.xml test-data/nCoV-2019.amplicons.bed test-data/nCoV-2019.scheme.bed
diffstat 4 files changed, 376 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/primer_scheme_to_amplicon_intervals.py	Wed Mar 18 03:00:48 2020 +0000
@@ -0,0 +1,54 @@
+#!/usr/bin/env python
+
+from __future__ import print_function
+
+import argparse
+import csv
+import json
+
+
+def parse_primer_scheme(primer_scheme):
+    primer_pairs = {}
+    fieldnames = [
+        'ref',
+        'start',
+        'end',
+        'primer_name',
+        'pool',
+    ]
+    primer_pair_names = set()
+    with open(primer_scheme) as f:
+        reader = csv.DictReader(f, delimiter="\t", quotechar='"', fieldnames=fieldnames)
+        for row in reader:
+            pair_name = '_'.join(row['primer_name'].split('_')[0:2])
+            left_right = row['primer_name'].split('_')[2].lower()
+            if pair_name not in primer_pairs.keys():
+                primer_pairs[pair_name] = {'ref': row['ref']}
+                primer_pairs[pair_name][left_right] = {
+                    'start': int(row['start']),
+                    'end': int(row['end']),
+                }
+            else:
+                primer_pairs[pair_name][left_right] = {
+                    'start': int(row['start']),
+                    'end': int(row['end']),
+                }
+            
+    return primer_pairs
+
+
+def main(args):
+    primer_pairs = parse_primer_scheme(args.primer_scheme)
+    # print(json.dumps(primer_pairs))
+    for name, primers in primer_pairs.items():
+        ref = primers['ref']
+        start = str(primers['left']['start'])
+        end = str(primers['right']['end'])
+        print('\t'.join([ref, start, end, name]))
+
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser()
+    parser.add_argument("primer_scheme", help="Input: Primer Scheme (.bed)")
+    args = parser.parse_args()
+    main(args)
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/primer_scheme_to_amplicon_intervals.xml	Wed Mar 18 03:00:48 2020 +0000
@@ -0,0 +1,28 @@
+<tool id="primer_scheme_to_amplicon_intervals" name="Primer Scheme to Amplicon Intervals" version="0.1.0+galaxy0">
+    <description>
+        Primer Scheme to Amplicon Intervals
+    </description>
+    <requirements>
+    </requirements>
+    <command detect_errors="exit_code">
+        <![CDATA[
+          python '${__tool_directory__}/primer_scheme_to_amplicon_intervals.py'
+            '${primer_scheme}'
+            > '${amplicon_intervals}'
+        ]]>
+    </command>
+    <inputs>
+        <param name="primer_scheme" type="data" format="bed" label="Primer Scheme" />
+    </inputs>
+    <outputs>
+        <data name="amplicon_intervals" label="Amplicon Intervals" format="bed" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="primer_scheme" value="nCoV-2019.scheme.bed" />
+            <output name="amplicon_intervals" value="nCoV-2019.amplicons.bed" />
+        </test>
+    </tests>
+    <help><![CDATA[
+    ]]></help>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/nCoV-2019.amplicons.bed	Wed Mar 18 03:00:48 2020 +0000
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/nCoV-2019.scheme.bed	Wed Mar 18 03:00:48 2020 +0000
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