ncbi_db

Collection of commands to query or process NCBI data

Installation

conda install -c mmariotti -c conda-forge -c etetoolkit ncbi_db

Tools

These command line tools are available:

• ncbi_assembly search and download assemblies/genomes for any species/lineage, or its annotation/proteome
• ncbi_sequences search and download nucleotide/protein sequences or their metadata
• ncbi_pubmed search and format ncbi pubmed entries
• ncbi_taxonomy search ncbi taxonomy for species or lineages
• ncbi_taxonomy_tree obtain a tree from ncbi taxonomy for a set of input species
• ncbi_search generic search tool for any ncbi DB
• parse_genbank parse a genbank flat file; requires installation of GBParsy

Run any tool with option -h to display its usage.

Most tools require internet, as they connect online to ncbi.

Using ncbi_db as module

To use these functionalities from another python module, import them from ncbi_db and run their "main" function providing the same arguments as you would on the command line, but in form of dictionary. Use option 'silent' to avoid printing results on screen. For example:

from ncbi_db import ncbi_sequences
arguments={'m':'P', 'f':1, 'I':'AAB88790', 'silent':1}
results=ncbi_sequences.main(arguments)
print(results)

{'AAB88790':
 ['AAB88790.1 gi|2411487|gb|AAB88790.1| selenophosphate synthetase [Drosophila melanogaster]',
 'MSYAADVLNSAHLELHGGGDAELRRPFDPTAHDLDASFRLTRFADLKGRGCKVPQDVLSKLVSALQQDYSAQDQEPQFLNVAIPRIGIGLDCSVIPLRHGGLCLVQTTDFFYPIVDDPYMMGKIACANVLSDLYAMGVTDCDNMLMLLAVSTKMTEKERDVVIPLIMRGFKDSALEAGTTVTGGQSVVNPWCTIGGVASTICQPNEYIVPDNAVVGDVLVLTKPLGTQVAVNAHQWIDQPERWNRIKLVVSEKNVRKAYHRAMNSMARLNRVAARLMHKYNAHGATDITGFGLLGHAQTLAAHQKKDVSFVIHNLPVIAKMAAVAKACGNMFQLLQGHSAETSGGLLICLPREQAAAYCKDIEKQEGYQAWIIGIVEKGNKTARIIDKPRVIEVPAKD']}

Developers

Marco Mariotti https://github.com/marco-mariotti

Didac Santesmasses https://github.com/didacs