[BioPython] Local Blast Output

[Sebastian Bassi]

On 4/13/07, JASON HORTIATIS <jhortia1 at jhu.edu> wrote:
> I'm an undergraduate using biopython to run local blast searches and I'm trying to find out how to save the entire sequence of each protein hit directly to a file.  I have only managed to be able to print the portion of the sequence that matches the query using hsp.sbjct[0:].  My goal is to use the search results from one blast run as a database to search against for a subsequent run so a fasta file is needed for each hit of the first run.
> Thanks for the help!

You can only parse from the BLAST result what is inside the BLAST
output. And there is no the whole sequence In such output, just the
portion you've retrieved. You may need to parse the GID of the protein
and then look for it in your BLAST DB (using fastacmd).
Or you may use PSI-BLAST as an alternative.