Mercurial > repos > earlhaminst > ete
comparison ete_lineage_generator.py @ 9:b29ee6a16524 draft
"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 17c65045b726d0695814bfe761e534f6521786f1"
| author | earlhaminst |
|---|---|
| date | Tue, 20 Oct 2020 15:10:40 +0000 |
| parents | f1eca1158f21 |
| children | 2db72467da51 |
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| 8:16e925bf567e | 9:b29ee6a16524 |
|---|---|
| 39 taxid: a taxid (int) | 39 taxid: a taxid (int) |
| 40 ranks: list of ranks (should be initialized with "NA" x number of levels of interest) | 40 ranks: list of ranks (should be initialized with "NA" x number of levels of interest) |
| 41 RANK_IDX: mapping from rank names to indices (distance to root/leaf?) | 41 RANK_IDX: mapping from rank names to indices (distance to root/leaf?) |
| 42 lower: use lower taxa for filling "NA"s | 42 lower: use lower taxa for filling "NA"s |
| 43 """ | 43 """ |
| 44 lineage = ncbi.get_lineage(taxid) | 44 lineage_taxids = ncbi.get_lineage(taxid) |
| 45 lineage_ranks = ncbi.get_rank(lineage) | 45 lineage_ranks = ncbi.get_rank(lineage_taxids) |
| 46 lineage_names = ncbi.get_taxid_translator(lineage, try_synonyms=True) | 46 lineage_names = ncbi.get_taxid_translator(lineage_taxids, try_synonyms=True) |
| 47 if lower: | 47 if lower: |
| 48 lineage.reverse() | 48 lineage_taxids.reverse() |
| 49 for l in lineage: | 49 for parent_taxid in lineage_taxids: |
| 50 if not lineage_ranks[l] in RANK_IDX: | 50 parent_rank = lineage_ranks[parent_taxid] |
| 51 if parent_rank not in RANK_IDX: | |
| 51 continue | 52 continue |
| 52 if ranks[RANK_IDX[lineage_ranks[l]]] != "NA": | 53 parent_rank_index = RANK_IDX[parent_rank] |
| 54 if ranks[parent_rank_index] != "NA": | |
| 53 continue | 55 continue |
| 54 ranks[RANK_IDX[lineage_ranks[l]]] = lineage_names[l] | 56 ranks[parent_rank_index] = lineage_names[parent_taxid] |
| 55 | 57 |
| 56 | 58 |
| 57 # get command line options | 59 # get command line options |
| 58 parser = optparse.OptionParser() | 60 parser = optparse.OptionParser() |
| 59 parser.add_option('-s', '--species', dest="input_species_filename", | 61 parser.add_option('-s', '--species', dest="input_species_filename", |