Collection of scripts that wrap the Entrez Bio python module, to query and download portions of NCBI databases
Project description
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
Right now these tools are available:
- ncbi_lib.py library of functions; not to be executed
- ncbi_db_info.py simply to display the available fields in any ncbi DB, browsable through the BioPython tools
- ncbi_assembly.py to browse the available assemblies/genomes for any species or lineage, including their annotation/proteome, and possibly download them in a local folder
- parse_genbank.py parse a gbf file to extract selected entries. Requires GBParsy module
- ncbi_pubmed.py wrapper to ncbi pubmed search engine; it can format results for bibliography
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