[BioPython] running primer3 with multiple sequences

[Maqbool, Nauman]

Hi

I am trying to run eprimer3 using biopython and am not sure how to input
multiple options. E.g. if I am reading in a fasta file with hundreds of
sequences with different primer design parameters for each sequence, do
I have to hard code the parameters individually for each sequence?

In the example below:

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

def get_primers(fasta_record, start, end):
    open("in.pr3", "w").write(str(fasta_record) + "\n")
    primer_cl = Primer3Commandline()
    primer_cl.set_parameter("-sequence", "in.pr3")
    primer_cl.set_parameter("-outfile", "out.pr3")
    primer_cl.set_parameter("-productsizerange", "350,500")
    primer_cl.set_parameter("-target", "%s,%s" % (start, end))
    result, r, e = generic_run(primer_cl)
    parser = Primer3Parser()
    return parser.parse(open("out.pr3"))

def main(fasta_file, output_file):
    output_handle = open(output_file, "w")
    output_handle.write("name,forward_primer,reverse_primer\n")
    parser = Fasta.RecordParser()
    iterator = Fasta.Iterator(open(fasta_file), parser)
    while 1:
        cur_record = iterator.next()
        if not(cur_record): break
        primer_record = get_primers(cur_record, 100, 250)
        if len(primer_record.primers) > 0:
            primer = primer_record.primers[0]
            output_handle.write("%s,%s,%s\n" % (
            cur_record.title, primer.forward_seq,
            primer.reverse_seq))
        else:
            print "No primers found for %s" % cur_record.title

 
the start and end positions, i.e. the target area, to be included in the
product, remains the same (100 to 250 in this case), how do I change
these if I have a different target area for different sequences?

Also, how do I use biopython if I give the sequences and parameters in
the format below, rather than using a fasta file?

PRIMER_SEQUENCE_ID=test_seq1
SEQUENCE=atgatgatgtnnnnnnnnntgatgatgatgcaccatagatgatcacacaccattaaacatcat
catcttgatgatgatgcaccatagatgatcacacaccattaaacatcatcatcttaaacatcatcatcttga
tgatgatgcaccatagatgatcacacaccataaacatcatcatctgatgatgatgcaccatagatgatcaca
caccattaaacatcatcatcttaaacatcatcatcttgatgatgatgcaccatagatgatcacacaccatta
aacatcatcatcttaaacatcatcatcttgatgatgatgcaccatagatgatcacacacca
INCLUDED_REGION=150,329
PRIMER_OPT_SIZE=19
PRIMER_MIN_SIZE=17
PRIMER_MAX_SIZE=22
PRIMER_PRODUCT_SIZE_RANGE=64-629
PRIMER_EXPLAIN_FLAG=1
=

Thanks a lot

Nauman
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