[Biopython] pass a variable to a blast cmd

Frederico Moraes Ferreira ferreirafm at usp.br
Tue Jun 18 14:12:33 UTC 2013


Hi there,
Is there a clever way of passing a variable to the blast_cline command like:

  blast_cline = NcbiblastpCommandline((cmd = "blastp", task = 
"blastp-short",
                                         query = inf, matrix = "PAM30",
                                         outfmt = "5", db = "%s",
                                         remote = True, comp_based_stats 
= "0",
                                          out = "blast_out.xml") % database)

or should I have to have one command to each option.
Best,
Fred









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