[BioPython] Problems with Emboss.Primer3

[Stefanie Lück]

Hi!

I'm trying to generate a Primer3 file but I have some problems because my output file is allways empty.
Unfortunatly I don't get an error message.

Here's my code:

from Bio import Fasta
from Bio.Emboss.Applications import Primer3Commandline
from Bio.Application import generic_run
from Bio.Emboss.Primer import Primer3Parser
        
primer_cl = Primer3Commandline()
primer_cl.set_parameter("-sequence", "p3input.txt")
primer_cl.set_parameter("-outfile", "out.pr3")
primer_cl.set_parameter("-productsizerange", "350,10000")
primer_cl.set_parameter("-target", "%s,%s" % (50, 500))
result, messages, errors = generic_run(primer_cl)

p3input.txt looks like this:

PRIMER_SEQUENCE_ID=HF15E08r
SEQUENCE=GCATGTAATAATGCCAAAGCTCACAGCTGCAGTTGAATCTTGGGACCCGCGGAGCGAGAATGTACCAATCCATGTATGGGTACACCCATGGCTGCCAACTCTAGGGCAAAGGATAGATACACTGTGCCACTCTATCCGGTACAAGCTGAGTAGTGTCCTCCAATTATGGCAAGCTCACGATTCATCAGCTTATGCTGTGCTATCTCCATGGAAGGGTGTATTTGATCCAGCAAGTTGGGAAGACTTGATAGTGCGTTATATCATTCCTAAACTGAAAATGGCACTCCAGGAGTTCCAGATTAACCCAGCAAGCCAAAAGTTTGACCAGTTTAACTGGGTTATGATCTGGGCTTCTGCTGTCCCGGTACACCATATGGTCCATATGTTGGAAGTTGATTTCTTTAGCAAGTGGCAGCTGGTTTTGTACCATTGGCTGAGCTCACCAAATCCTGATTTCAATGAGATAATGAATTGGTAT
PRIMER_PRODUCT_SIZE_RANGE=500-1000 450-500 400-450 350-400 300-350 250-300 200-250 150-200
PRIMER_OPT_TM=60.0
PRIMER_MIN_TM=58.0
PRIMER_MAX_TM=65.0
PRIMER_MAX_DIFF_TM=3.0
PRIMER_DNA_CONC=420
PRIMER_NUM_RETURN=1
=
PRIMER_SEQUENCE_ID=HO05B04S
SEQUENCE=GAAAACCCAATGACAGTAGGATGACAAGGGAAAACTGGTGAGCAACGTCGTAGTCGGGGTTACCACCGGCGGGAAAAAGTAGCAAAACTATGTCATGTCTTATAATCTGGAGTTGGGAACACCTTGTATTATACTCGTGTCTGGGGATCGACCGATCGGTCGCGTAGAAGAAAAACCCAAAGCGCGGAAATGGACCGCGCCAACAAAAAAAGAGGGTGCGGGTGTGGATAATATGGAGAAGAACTGTATTTTGCTTACCCCCTTGATTCTTTTGTATGTAAAATGTGGGCACTGTCAGACCTCACTGTGTGATCAAATCCTCTCTGTCCTGTCCTGTCCTGAAGGGGCCTCTCGTTCTGGATGAATAAACAGCAAATAACTTTGCGTGTGGCTGGCCCCACCTGTCGGTGATTGGTAATTAAAACGACGGTAATTGTTGTG
PRIMER_PRODUCT_SIZE_RANGE=500-1000 450-500 400-450 350-400 300-350 250-300 200-250 150-200
PRIMER_OPT_TM=60.0
PRIMER_MIN_TM=58.0
PRIMER_MAX_TM=65.0
PRIMER_MAX_DIFF_TM=3.0
PRIMER_DNA_CONC=420
PRIMER_NUM_RETURN=1

...

Does someone has idea what's the problem?

Thanks in advance,
Stefanie