Are there wrappers for blastdb_aliastool, blastdbcmd in Biopython Blast module? Any alternatives?

Question

[bsmith4133]

I'm trying to make a gene pipeline using the standalone Blast application, and I've been using the Bio.Blast.Applications module. In the BioPython documentation, there doesn't seem to be wrappers for tools such as blastdb_aliastool and blastbcmd. Does anyone know if they exist? If not, would the best alternative be to use the Python subprocess module for command line use?

Thanks!

Answer 1

[Istvan Albert]

both of these commands are unrelated to the main function of blast, and are quite quirky at what parameter combinations they support and what output they produce. Hence unlikely any package would support them directly.

I would recommend invoking them as a subprocess module.