gtax 0.1.0

Gtax generate a taxonomy sequence database by genomes

GTax

GTax python package provides tools for the creation of the GTax sequence-based database. This database includes one assembly per organism deposited in the NCBI Genomes database. The sequences are organized by 19 taxonomic levels from superkindom to clades. Python pickle files are also provided with a graph data structure for the taxonomic tree.

Read the Docs at: https://gtax.readthedocs.io/

Current version

The current public version is available in GCP for download. You need to use your GCP project as this bucket uses Requester Pays option.

https://console.cloud.google.com/storage/browser/gtax-database/

gsutil -u <you-GCP-project> -m cp -r gs://gtax-database/<latest_version> .

The database is comprised of two folder: blastdb and fasta. The blastdb folder include the BLAST indexes for BLAST searches. The fasta folder includes the FASTA files for the taxonomy groups and two Python Objects in pickle files (taxonomy.pickle and taxonomy_groups.pickle) which are used to load all GTax metadata into the Taxonomy class

from gtax.taxonomy import Taxonomy
taxonomy = Taxonomy(tax_pickle_file='taxonomy.pickle', group_pickle_file = 'taxonomy_groups.pickle')

Output:

2464341 taxonomies loaded
bacteria Node: 537498 Sequences: 19435
archaea Node: 14266 Sequences: 798
liliopsida Node: 48464 Sequences: 317
eudicotyledons Node: 153108 Sequences: 1077
viridiplantae Node: 48003 Sequences: 185
fungi Node: 186994 Sequences: 914
arthropoda Node: 912789 Sequences: 2596
neoteleostei Node: 31205 Sequences: 1610
actinopterygii Node: 22514 Sequences: 1258
glires Node: 5490 Sequences: 2346
primates Node: 1101 Sequences: 673
carnivora Node: 783 Sequences: 437
artiodactyla Node: 1200 Sequences: 487
amphibia Node: 13009 Sequences: 122
sauropsida Node: 32051 Sequences: 1476
sarcopterygii Node: 4941 Sequences: 376
chordata Node: 4122 Sequences: 400
eukaryota Node: 194114 Sequences: 896
viruses Node: 234108 Sequences: 14233

Public Domain notice

National Center for Biotechnology Information.

This software is a "United States Government Work" under the terms of the United States Copyright Act. It was written as part of the authors' official duties as United States Government employees and thus cannot be copyrighted. This software is freely available to the public for use. The National Library of Medicine and the U.S. Government have not placed any restriction on its use or reproduction.

Although all reasonable efforts have been taken to ensure the accuracy and reliability of the software and data, the NLM and the U.S. Government do not and cannot warrant the performance or results that may be obtained by using this software or data. The NLM and the U.S. Government disclaim all warranties, express or implied, including warranties of performance, merchantability or fitness for any particular purpose.

Please cite NCBI in any work or product based on this material.