[Biopython-dev] [Bug 3173] New: Bio.Emboss.Primer3 parser incompatibility with Primer3 version 2.2.3

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http://bugzilla.open-bio.org/show_bug.cgi?id=3173

           Summary: Bio.Emboss.Primer3 parser incompatibility with Primer3
                    version 2.2.3
           Product: Biopython
           Version: 1.55
          Platform: Macintosh
        OS/Version: Mac OS
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Other
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: jp.verta at gmail.com


I'm running Biopython 1.55, Python 2.6 and EMBOSS version 6.3.1 on MacOS X 10.6
Snow Leopard.

The Bio.Emboss.Primer3 parser seems to be incompatible with the newer version
2.2.3 of the Whitehead Primer3 program and the corresponding Emboss eprimer3
program output. The parser output for the reverse primer seems to contain all
Primer -class members (primer.reverse_tm, primer.reverse_gc etc.) except the
reverser primer sequence (primer.reverse_seq). Yet the eprimer3 output seems
identical to that of old versions (see the output.pr3 -files attached). 

Here is an example code for designing primers for a set of fasta sequences. 

>>>

 def design_primers(fasta_file, output_file):
    from Bio import SeqIO
    from Bio.Emboss.Applications import Primer3Commandline
    from Bio.Emboss import Primer3
    output = open(output_file, "w")
   
output.write("name,forward_primer,reverse_primer,forward_tm,reverse_tm,product_size\n")
    for seq_record in SeqIO.parse(fasta_file, "fasta"):
        if not(seq_record): 
            break
        open("sequence",
"w").write(">"+str(seq_record.id)+"\n"+str(seq_record.seq)+"\n")
        primer_cl = Primer3Commandline(sequence="sequence")
        primer_cl.explainflag = True
        primer_cl.osizeopt=20
        primer_cl.psizeopt=200
        primer_cl.otm=65
        primer_cl.maxtm=70
        primer_cl.mintm=60
        primer_cl.gcclamp=1 #required number of Gs or Cs at the 3' end of the
primer
        primer_cl.outfile = "output.pr3"
        primer_cl()
        output_handle = open("output.pr3","r")
        primer_record = Primer3.read(output_handle)
        if len(primer_record.primers) > 0:
            primer = primer_record.primers[0] 
            output.write("%s,%s,%s,%s,%s,%s\n" % (seq_record.id,
primer.forward_seq, primer.reverse_seq,
primer.forward_tm,primer.reverse_tm,primer.size))
        else: 
            print "No primers found for %s" % seq_record.id

>>>

This code, when executed on a file of fasta-sequences gives and output -file
with forward and reverse primer id, sequence, tm and size separated by commas.
When I execute it with the Primer3-2.2.3 and compatible eprimer3 versions, the
field for the reverse primer sequence appears blank.

I will attach the Primer3-2.2.3 compatible eprimer3 file to this report.


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