A toolkit for analyzing Taxonomy
Project description
TaxonTools
TaxonTools can help you use NCBI Taxonomy database
Installation
pip install taxontools
Usage
prepare: Download NCBI Taxonomy database and convert it to sqlite format
Download NCBI Taxonomy database
wget ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz
Convert NCBI database to sqlite format
tar -zxvf taxdump.tar.gz
TaxonTools StoreTaxonDB ./taxdump taxdump.db
ID2Lineage
TaxonTools ID2Lineage -q 3701,4530 taxdump.db
TODO
# --------------------------------------------
# command detail
if args_dict["subcommand_name"] == "ID2Lineage":
from toolbiox.src.xuyuxing.tools.taxontools import ID2Lineage_main
ID2Lineage_main(args)
elif args_dict["subcommand_name"] == "StoreTaxonDB":
from toolbiox.lib.xuyuxing.evolution.taxonomy import build_taxon_database, store_tax_record_into_sqlite
tax_record_dict = build_taxon_database(args.tax_dir)
store_tax_record_into_sqlite(tax_record_dict, args.tax_db_file)
elif args_dict["subcommand_name"] == "CommonTree":
from toolbiox.src.xuyuxing.tools.taxontools import CommonTree_main
CommonTree_main(args)
elif args_dict["subcommand_name"] == "Name2Lineage":
from toolbiox.src.xuyuxing.tools.taxontools import Name2Lineage_main
Name2Lineage_main(args)
elif args_dict["subcommand_name"] == "RankStat":
from toolbiox.src.xuyuxing.tools.taxontools import RankStat_main
RankStat_main(args)
elif args_dict["subcommand_name"] == "ExcludeTaxon":
"""
class abc():
pass
args = abc()
args.tax_dir = '/lustre/home/xuyuxing/Database/genome2020/genome/info/NCBI/taxonomy'
args.root_taxon_id = '73496'
args.taxon_id = '40553'
"""
from toolbiox.src.xuyuxing.tools.taxontools import ExcludeTaxon_main
ExcludeTaxon_main(args)
elif args_dict["subcommand_name"] == "DiamondTaxonAssign":
"""
class abc():
pass
args = abc()
args.blast_results = '/lustre/home/xuyuxing/Database/Cuscuta/Cau/genomev1.1/gene_taxon/Cuscuta.pt.v1.1.fasta.bls'
args.tax_dir = '/lustre/home/xuyuxing/Database/NCBI/nr/2020/taxdmp'
args.output_file = '/lustre/home/xuyuxing/Database/Cuscuta/Cau/genomev1.1/gene_taxon/Cuscuta.pt.v1.1.fasta.taxon'
args.num_threads = 56
"""
from toolbiox.src.xuyuxing.tools.taxontools import DiamondTaxonAssign_main
DiamondTaxonAssign_main(args)
Project details
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