Mercurial > repos > iuc > checkm_tree

comparison format_taxon_list.py @ 0:9b2790bca5b5 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
author iuc
date Fri, 29 Jul 2022 20:29:27 +0000
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-1:000000000000 0:9b2790bca5b5
1 from pathlib import Path
2
3 from checkm.taxonParser import TaxonParser
4 from checkm.util.taxonomyUtils import taxonomicRanks
5
6 if __name__ == '__main__':
7 tool_data_dp = Path('tool-data')
8
9 # get all available marker sets
10 taxonParser = TaxonParser()
11 taxonMarkerSets = taxonParser.readMarkerSets()
12
13 # create a table per rank
14 for rank in taxonomicRanks:
15 rank_fp = tool_data_dp / Path("%s.loc.sample" % rank)
16 with rank_fp.open('w') as rank_f:
17 rank_f.write('# File generated by format_taxon_list.py script\n')
18 rank_f.write('# taxon\tdescription\n')
19 for taxon in sorted(taxonMarkerSets[rank]):
20 markerSet = taxonMarkerSets[rank][taxon]
21 numMarkers, numMarkerSets = markerSet.size()
22 rank_f.write('{taxon}\t{taxon} ({markerSet.numGenomes} genomes, {numMarkers} marker genes, {numMarkerSets} marker sets)\n')