[Biopython] PSI-BLAST

[Eric Talevich]

On Wed, Jul 20, 2011 at 11:30 AM, molly mutant
<mollymutant at googlemail.com>wrote:

> Can anyone please share the functioning codes for PSI-BLAST using NCBI
> commandline or suggest me the source from where i can get it?? i am in an
> urgent need of it :( and i can not find the problem with my command/code.
>
> Regards,
> Molly
>
> On Wed, Jul 20, 2011 at 4:19 PM, molly mutant <mollymutant at googlemail.com
> >wrote:
>  > the following error occurs :
> > Bio.Application.ApplicationError: Command 'psiblast -out
> NP_012649_psi.xml
> > -outfmt 7 -query NP_012649.fasta -db refseq_protein -evalue 10 -out_pssm
> > NP_012649_pssm' returned non-zero exit status 127, '/bin/sh: psiblast:
> not
> > found'
> >
> > I think this error stands for that the command is not found, which means
> > that my command is incorrect, am i right??
>

To follow up on what João wrote, the important error is:
'/bin/sh: psiblast: not found'

Which means that psiblast is not installed correctly on your system. If you
try running just that command on the command line:
psiblast -out NP_012649_psi.xml -outfmt 7 -query NP_012649.fasta -db
refseq_protein -evalue 10 -out_pssm NP_012649_pssm

will also report an error, even without using Python.

So, try making sure psiblast is available on your system path ($PATH). The
command "which psiblast" should print where the executable is, if it can be
found.

Or, if you don't want to mess with $PATH, you can include the complete path
to the psiblast executable:
psi_cline = NcbipsiblastCommandline('/usr/local/bin/psiblast', db = ...


Cheers,
Eric