[Biopython] PSI-BLAST

[malvika sharan]

Thanks Senthil, but that is what i mentioned that i am trying to use
wrappers in Bio.Blast.Applications module. It just does not seem to work. I
have the whole Biopython installed and i am using Python 2.7.

the problem occurs while importing itself, i mentioned the error as well.
here is the whole error description:
Traceback (most recent call last):
    File "psiBlast.py", line 6, in <module>
        from Bio.Blast.Applications import NcbipsiblastCommandline
ImportError: cannot importname NcbipsiblastCommandline

i just cant figure out why.


On Mon, Jul 18, 2011 at 12:23 AM, Senthil Kumar M
<senthil.debian at gmail.com>wrote:

> On Sun, Jul 17, 2011 at 2:53 PM, malvika sharan <malvikasharan at gmail.com>
> wrote:
> > Hi All,
> >
> > I am trying to code WWW version of PSI-BLAST. My intention is to
> integrate
> > PSI-Blast in my tool in order to find distant homologs.
> >
> > i some how can not run the commandline version of psi blast (from
> > Bio.Blast.Applications import *NcbipsiblastCommandline*) as it states the
> > error
> > *" **Python* error: ImportError: *cannot* import *name
> > **NcbipsiblastCommandline
> > "*
> > *
> > *
> > *There are not much information available about it. Can somebody figure
> out
> > why?*
> > *
> > *
> > *Malvika*
> > *
> > *
>
> Hi,
>
> According to the Biopython tutorial
> http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc93 (2 April
> 2011 version):
>
> "You can run the standalone verion of PSI-BLAST (the legacy NCBI
> command line tool blastpgp, or its replacement psiblast) using the
> wrappers in Bio.Blast.Applications module.
> At the time of writing, the NCBI do not appear to support tools
> running a PSI-BLAST search via the internet."
>
> HTH,
>
> Senthil
>
> -/
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>