[BioPython] Re: emboss commandline via python

[Andreas Dahl]

hi brad,

thanks for your help and some other people from the maillist. :o)
the solution was to call the absolute path of eprimer3:

from Bio.Emboss.Applications import Primer3Commandline
from Bio.Emboss.Primer import Primer3Parser
from Bio.Application import generic_run

open("in.pr3", "w").write(str(fasta_record) + "\n")
primer_cl = Primer3Commandline(cmd =/package/emboss/bin-i386/eprimer3")
primer_cl.set_parameter("-sequence", "in.pr3")
primer_cl.set_parameter("-outfile", "out.pr3")
primer_cl.set_parameter("-target", "%s,%s" % (start, end))
print str(primer_cl)
result, r, e = generic_run(primer_cl)
...

regards - andreas