[Biopython] Read and Parse EMBOSS primer3-eprimer32

Ivaylo Stoimenov ivaylo.stoimenov at gmail.com
Wed Oct 10 07:00:55 EDT 2012


Hi,

I have a problem of using Read and Parse functions when it comes to EMBOSS
Primer3 (or eprimer32 wrapper). I would like to skip writing files but
hijacking the output of Primer3 to a variable (object). Here is some part
of the code, which does not work:

from Bio.Emboss import Primer3
from Bio.Emboss.Applications import Primer3Commandline
import sys
...
cline = Primer3Commandline(sequence=combined_frame, auto=True, task =1)
cline.explainflag = True
cline.prange="100-150"
cline.outfile = "stdout"

ggg = cline()
primer_record = Primer3.read(sys.stdout or ggg[0] or ...)
print primer_record
...

What I am doing wrong. The output of cline() is a tuple, but I would like
to read or parse the first element. The problem is that Primer3.read and
Primer3.parse expect file handles. Any advice would be highly appreciated.

Kind regards,
Ivaylo


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