| Previous changeset 3:7f781286b55f (2020-06-05) Next changeset 5:5e668dc9f379 (2021-05-19) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 693df287d23b0fd9dfd134b41d401a438c3f5ad6" |
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added:
completemask.py sanitize_bed.py test-data/covid19/ARTIC-V1-bad.bed |
| b |
| diff -r 7f781286b55f -r 78bbd17d0703 completemask.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/completemask.py Mon Jun 22 07:31:22 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') |
| b |
| diff -r 7f781286b55f -r 78bbd17d0703 sanitize_bed.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sanitize_bed.py Mon Jun 22 07:31:22 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) |
| b |
| diff -r 7f781286b55f -r 78bbd17d0703 test-data/covid19/ARTIC-V1-bad.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/covid19/ARTIC-V1-bad.bed Mon Jun 22 07:31:22 2020 -0400 |
| b |
| b'@@ -0,0 +1,196 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