[Biopython] Bio.Emboss.Primer3 -parser and Primer3 2.2.3

[Jukka-Pekka Verta]

Hello,

I'm having trouble parsing out the Bio.Emboss.Primer3Commandline output when using the Whitehead Institute Primer3 version 2.2.3 (and a compatible eprimer3 version). The parser (Bio.Emboss.Primer3) does not write out the reverse primer sequence i.e. the Primers -class member "reverse_seq" is empty. The parser worked fine with the 1.1.4 version of Primer3 and the compatible eprimer3.

The output of the primer3-2.2.3 compatible eprimer3 -version looks nearly identical to the old distributions:


# EPRIMER3 RESULTS FOR GQ0197_O05.1

# FORWARD PRIMER STATISTICS:
# considered 5541
# GC content failed 14
# GC clamp failed 573
# low tm 4213
# high any compl 10
# high end compl 40
# long poly-x seq 8
# ok 683

# REVERSE PRIMER STATISTICS:
# considered 5629
# GC content failed 211
# GC clamp failed 564
# low tm 4100
# high end compl 10
# long poly-x seq 12
# ok 732

# PRIMER PAIR STATISTICS:
# considered 6607
# unacceptable product size 6551
# high end compl 20
# ok 36

#                      Start  Len   Tm     GC%   Sequence


     FORWARD PRIMER     799   23  63.93  69.57  AGCCACCAGGGGGTGCTCTCCAG

     REVERSE PRIMER     979   20  62.11  70.00  TGGCGACTCGGCCCATGCAC


     FORWARD PRIMER     799   20  60.18  70.00  AGCCACCAGGGGGTGCTCTC

     REVERSE PRIMER     979   20  62.11  70.00  TGGCGACTCGGCCCATGCAC


     FORWARD PRIMER     800   22  63.01  72.73  GCCACCAGGGGGTGCTCTCCAG

     REVERSE PRIMER     975   23  64.22  69.57  GGCGACTCGGCCCATGCACTGTC


     FORWARD PRIMER     799   23  63.93  69.57  AGCCACCAGGGGGTGCTCTCCAG

     REVERSE PRIMER     975   23  64.22  69.57  GGCGACTCGGCCCATGCACTGTC


...and that's why I'm kinda lost. Thank you for your help!

JP Verta