| Previous changeset 4:f95f403841ad (2020-06-22) Next changeset 6:147465efa99c (2021-06-10) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b" |
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modified:
macros.xml |
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added:
prepare_amplicon_info.py |
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| diff -r f95f403841ad -r 49236b03e4fd macros.xml --- a/macros.xml Mon Jun 22 07:29:41 2020 -0400 +++ b/macros.xml Wed May 19 16:49:13 2021 +0000 |
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| @@ -1,9 +1,8 @@ <macros> - <token name="@VERSION@">1.2.2</token> + <token name="@VERSION@">1.3.1</token> <xml name="requirements"> <requirements> <requirement type="package" version="@VERSION@">ivar</requirement> - <requirement type="package" version="1.9">samtools</requirement> <yield /> </requirements> </xml> |
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| diff -r f95f403841ad -r 49236b03e4fd prepare_amplicon_info.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/prepare_amplicon_info.py Wed May 19 16:49:13 2021 +0000 |
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| @@ -0,0 +1,57 @@ +#!/usr/bin/env python + +# extends ivar trim's amplicon info parsing abilities +# to include calculation of amplicon regions from +# sets of nested (more than two) primers + +import sys + + +# parse primers and their start positions from BED file +primer_starts = {} +with open(sys.argv[1]) as i: + for line in i: + f = line.strip().split('\t') + try: + if f[5] == '+': + primer_starts[f[3]] = int(f[1]) + elif f[5] == '-': + primer_starts[f[3]] = int(f[2]) - 1 + else: + raise ValueError() + except (IndexError, ValueError): + sys.exit( + 'Primer BED file needs to be TAB-separated with the ' + 'following columns: ' + 'chrom, chromStart, chromEnd, name, score, strand, ' + 'where "chromStart", "chromEnd" need to be integer values ' + 'and "strand" needs to be either "+" or "-".' + ) + +# parse amplicon info and record outer primer names +with open(sys.argv[2]) as i: + ret_lines = [] + for line in i: + first = last = None + for pname in line.strip().split('\t'): + try: + primer_start = primer_starts[pname] + except KeyError: + sys.exit( + 'Amplicon info with primer name not found in ' + f'primer BED file: "{pname}"' + ) + if first is None or primer_start < primer_starts[first]: + first = pname + if last is None or primer_start > primer_starts[last]: + last = pname + if first == last: + sys.exit( + line + + 'is not a proper amplicon info line.' + ) + ret_lines.append(f'{first}\t{last}\n') + +# write amended amplicon info +with open(sys.argv[3], 'w') as o: + o.writelines(ret_lines) |