Metadata-Version: 2.1
Name: ncbi-db
Version: 0.0.4
Summary: Collection of scripts that wrap the Entrez Bio python module, to query and download portions of NCBI databases
Home-page: https://github.com/pypa/ncbi_db
Author: Marco Mariotti
Author-email: marco.mariotti@ub.edu
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.6
Description-Content-Type: text/markdown
Requires-Dist: biopython (>=1.46)
Requires-Dist: ete3
Requires-Dist: lxml
Requires-Dist: six

# ncbi_db
Collection of scripts that wrap the Entrez Bio python module.
Mainly to build your own copy of selected entries form the ncbi databases


## Installation

conda install -c mmariotti ncbi_db

## Tools

Right now these tools are available:

- *ncbi_assembly*       to browse (and download) the available assemblies/genomes for any species or lineage, including their annotation/proteome
- *ncbi_sequences*      search and download nucleotide/protein sequences or their metadata
- *ncbi_pubmed*         wrapper to ncbi pubmed search engine; it can format results for bibliography
- *ncbi_taxonomy*       search NCBI taxonomy
- *ncbi_taxonomy_tree*  
- *ncbi_db_info*        displays the available fields in any NCBI DB, useful before running ncbi_search
- *ncbi_search*         generic search tool for any NCBI DB
