[Biopython-dev] GI number for NcbiblastpCommandline

Brown, Tom Tom.Brown at enmu.edu
Wed Feb 19 20:42:19 UTC 2014

Currently using result_handle = NCBIWWW.qblast("blastp", "nr", blastGI) where blastGI = 113000 in the Biopython program and would like to convert it to a local blastp. Is there a way to specify the blastGi within NcbiblastpCommandline instead of having to provide a fasta file for blast?  What are my options.

from Bio.Blast.Applications import NcbiblastpCommandline
blastp_cline = NcbiblastpCommandline(query="sh3.fasta", db="nr", evalue=0.001, outfmt=5, out="sh3.xml")
stdout, stderr = blastp_cline()




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