[BioPython] Re: emboss commandline via python

[Brad Chapman]

Hi Andreas;

> i read you comments in the biopython maillist 
> (http://biopython.org/pipermail/biopython/2003-April/001269.html).
> i run your little progrom from the presentation (see below), but the 
> program crashes because it generates no file out.pr3.  ( [Errno 2] No 
> such file or directory: 'out.pr3')
>
> the in.pr3-file for the first sequence is built properly. if i run the 
> command for eprimer (eprimer3 -sequence in.pr3 -outfile out.pr3 -target 
> 50,100) in the original EMBOSS command line with this in.pr3-file, the 
> out.pr3-file is created properly.

Hmmm. I don't see anything wrong with the script from a quick
glance, and if I run it on a FASTA sequence I have here it worked
fine. Does it work for you on Tests/Fasta/f002? That file from
Biopython seems to work just fine for me. This way we can tell if
it's something with the input file, or with your system setup.

One thing you can do is print out the error message from running the
commandline. If modify get_primers to have:

     result, r, e = generic_run(primer_cl)
     print "Read output", r.read()
     print "Error output", e.read()

The read and error output from the program might give some clues as
to what is wrong.

Hope this helps some!
Brad