DatabaseBuddy
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.
| 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, file_of_accns, etc...>(optional) | Launch the live shell. Search terms and accessions can be provided here or from within the session once launched. |
| 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. |
