DatabaseBuddy

___ ## A friend that speaks database DatabaseBuddy is a command line program for searching the NCBI, UniProt, and Ensembl databases, sorting and filtering the results, and then fetching the full sequence records. Unlike the other BuddySuite modules, DatabaseBuddy is intended to run as a 'live shell'; it holds your data in memory so you can interact with it before writing to file.

Command line sequence manipulation tools

Functions

Function	Flag	Parameters	Brief Description
guess_database	-gd	<accn1,accn2,etc...>	Outputs the database each provided accession is most likely coming from.
live_shell	-ls	<accn1,accn2,search term,etc...>(optional)	Launch the live shell. Search terms and accessions can be provided here or from within the session once launched.

Modifying flags

Flag	Brief Description
-d --database	Select a specific database to search (ncbi_nuc, ncbi_prot, uniprot, ensembl). Default is all of them.
-o --out_format	Specify the supported format you want records returned in.