[BioPython] Primer3Commandline

[Brad Chapman]

Larry:
> > -----relevant part of my script-----
> > primer_cl=Primer3Commandline()
> > primer_cl.set_parameter("-sequence","in.pr3")
> > primer_cl.set_parameter("-outfile","out.pr3")
> > print str(primer_cl)    # i added this to see the command line that was used
> > result,r,e=generic_run(primer_cl)
> > ---------

Yair:
> There is actually an error in the ³Bio/Emboss/Applications.py² file. The
> application in Emboss is not called Primer3 but rather eprimer3. So all you
> have to do is to change line number 13 from:
> 
>     def __init__(self, cmd = "primer3"):
> 
> To:
> 
>     def __init__(self, cmd = "eprimer3"):

Thanks guys -- the emboss folks switched the name from primer3 to
eprimer3 on me (but eprimer3 actually makes more sense). Sorry for
not picking up on this earlier. I just fixed it in CVS.

> You should also notice that not all the options available in eprimer are
> listed in the parameter list. So if one of the options is missing just add
> it to the list.

Feel free to go ahead and add any options I missed (on anything) to
the CVS version. They're really easy to add and I definitely know
I'll probably miss some.

Thanks again!
Brad