Mercurial > repos > iuc > checkm_taxonomy_wf
diff format_taxon_list.py @ 0:91230b9141c1 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
author | iuc |
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date | Fri, 29 Jul 2022 20:32:07 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/format_taxon_list.py Fri Jul 29 20:32:07 2022 +0000 @@ -0,0 +1,22 @@ +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')