taxontools 0.1.0

A toolkit for analyzing Taxonomy

TaxonTools

TaxonTools can help you use NCBI Taxonomy database

Installation

pip install taxontools

usage

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

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)