[BioPython] Primer3Commandline

UToronto l.heisler at utoronto.ca
Fri Apr 25 16:08:14 EDT 2003

 I am new to Python (much more experience with Perl), and also fairly new to working in linux, and administering it (which I suspect may be a problem).

Interested in getting BioPython to work with Emboss/Primer 3 using Primer3Commandline
for designing primers to a large number of sequences.  

What i have"
primer 3 (0.9) is installed and working.  
emboss is installed and working and I can run primer 3 through emboss
biopython is also working

but...when I run a script similar to that in Brad Thompsons lectures, something does not work

-----relevant part of my script-----
print str(primer_cl)    # i added this to see the command line that was used

now when I run this, it loops through a set of 3 sequences with no errors (I've commented out parsing the results file for now).  But no out.pr3 file is created (i even tried running with a full path), making me suspicious that the primer3 has even run

printing out the command line I see     "primer3 -sequence in.pr3 -outfile out.pr3"
---if I try to run this from the prompt, it works and my out.pr3 file is created.
i also printed out the result value (from generic_run) and get <Bio.ApplicationResult instance at 0x83304c>

---a couple of other things.  i can run the emboss eprimer3 from its directory under Biopython, but not elsewhere.  but I set up an alias eprimer3 to this file, and an alias primer3 to the eprimer3 alias....so both primer3 and eprimer3 will invoke the program from wherever.

If anyone can give a hand in any way, it is much appreciated (although I am hoping to figure it out first)

Lawrence Heisler, PhD
Department of Laboratory Medicine and Pathobiology
Faculty of Medicine
University of Toronto
Phone: 416-946-7921
email: l.heisler at utoronto.ca
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