biopython v1.71.0 Bio.Blast.NCBIStandalone

Code for calling standalone BLAST and parsing plain text output (DEPRECATED).

Rather than parsing the human readable plain text BLAST output (which seems to change with every update to BLAST), we and the NBCI recommend you parse the XML output instead. The plain text parser in this module still works at the time of writing, but is considered obsolete and updating it to cope with the latest versions of BLAST is not a priority for us.

This module also provides code to work with the “legacy” standalone version of NCBI BLAST, tools blastall, rpsblast and blastpgp via three helper functions of the same name. These functions are very limited for dealing with the output as files rather than handles, for which the wrappers in Bio.Blast.Applications are preferred. Furthermore, the NCBI themselves regard these command line tools as “legacy”, and encourage using the new BLAST+ tools instead. Biopython has wrappers for these under Bio.Blast.Applications (see the tutorial).