Mercurial > repos > iuc > ivar_filtervariants
changeset 4:7fe36019c073 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 693df287d23b0fd9dfd134b41d401a438c3f5ad6"
| author | iuc |
|---|---|
| date | Mon, 22 Jun 2020 07:30:17 -0400 |
| parents | 2c47c138176e |
| children | 51afc8a64951 |
| files | completemask.py sanitize_bed.py test-data/covid19/ARTIC-V1-bad.bed |
| diffstat | 3 files changed, 244 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/completemask.py Mon Jun 22 07:30:17 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')
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sanitize_bed.py Mon Jun 22 07:30:17 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)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/covid19/ARTIC-V1-bad.bed Mon Jun 22 07:30:17 2020 -0400 @@ -0,0 +1,196 @@ +MN908947.3 30 54 nCoV-2019_1_LEFT NOINT + +MN908947.3 385 410 nCoV-2019_1_RIGHT NOINT - +MN908947.3 320 342 nCoV-2019_2_LEFT NOINT + +MN908947.3 704 726 nCoV-2019_2_RIGHT NOINT - +MN908947.3 642 664 nCoV-2019_3_LEFT NOINT + +MN908947.3 1004 1028 nCoV-2019_3_RIGHT NOINT - +MN908947.3 943 965 nCoV-2019_4_LEFT NOINT + +MN908947.3 1312 1337 nCoV-2019_4_RIGHT NOINT - +MN908947.3 1242 1264 nCoV-2019_5_LEFT NOINT + +MN908947.3 1623 1651 nCoV-2019_5_RIGHT NOINT - +MN908947.3 1573 1595 nCoV-2019_6_LEFT NOINT + +MN908947.3 1942 1964 nCoV-2019_6_RIGHT NOINT - +MN908947.3 1875 1897 nCoV-2019_7_LEFT NOINT + +MN908947.3 2247 2269 nCoV-2019_7_RIGHT NOINT - +MN908947.3 2181 2205 nCoV-2019_8_LEFT NOINT + +MN908947.3 2568 2592 nCoV-2019_8_RIGHT NOINT - +MN908947.3 2505 2529 nCoV-2019_9_LEFT NOINT + +MN908947.3 2882 2904 nCoV-2019_9_RIGHT NOINT - +MN908947.3 2826 2850 nCoV-2019_10_LEFT NOINT + +MN908947.3 3183 3210 nCoV-2019_10_RIGHT NOINT - 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