[BioPython] Problems with Emboss.Primer3
Stefanie Lück
lueck at ipk-gatersleben.de
Thu Nov 13 14:06:13 UTC 2008
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
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