Mercurial > repos > iuc > checkm_lineage_wf
view format_taxon_list.py @ 2:8345d273ba82 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 3ae2bd72f789518e95ef65b97e0e5ac90165e113
author | iuc |
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date | Mon, 02 Sep 2024 13:50:15 +0000 |
parents | 760dc0c0e689 |
children |
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from pathlib import Path from checkm.taxonParser import TaxonParser from checkm.util.taxonomyUtils import taxonomicRanks if __name__ == '__main__': tool_data_dp = Path('tool-data') # get all available marker sets taxonParser = TaxonParser() taxonMarkerSets = taxonParser.readMarkerSets() # create a table per rank for rank in taxonomicRanks: rank_fp = tool_data_dp / Path("%s.loc.sample" % rank) with rank_fp.open('w') as rank_f: rank_f.write('# File generated by format_taxon_list.py script\n') rank_f.write('# taxon\tdescription\n') for taxon in sorted(taxonMarkerSets[rank]): markerSet = taxonMarkerSets[rank][taxon] numMarkers, numMarkerSets = markerSet.size() rank_f.write('{taxon}\t{taxon} ({markerSet.numGenomes} genomes, {numMarkers} marker genes, {numMarkerSets} marker sets)\n')