Collection of scripts that wrap the Entrez Bio python module, to query and download portions of NCBI databases
Project description
ncbi_db
Collection of commands to query or process NCBI data
Installation
conda install -c mmariotti ncbi_db
Tools
These 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.
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ncbi_db-0.0.5-py3-none-any.whl
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