[Biopython] PSI-BLAST

[Eric Talevich]

On Sun, Jul 17, 2011 at 7:27 PM, malvika sharan <malvikasharan at gmail.com>wrote:

> My OS is mac, Python is 2.7 as mentioned,Biopython 1.50.
>

That's a very old version of Biopython. Are you able to install a more
recent version?


And well as i said that the the error shows at the import.
> import os, sys
> from Bio import SeqIO
> from Bio import Entrez
> from Bio.Blast import NCBIWWW*
> *from Bio.Blast.NCBIStandalone import PSIBlastParser
> *from Bio.Blast.Applications import NcbipsiblastCommandline*
> from Bio.Blast import NCBIXML
>

If the earlier imports of SeqIO and Entrez work, then
NcbipsiblastCommandline probably wasn't included in Biopython 1.50, I would
guess.



On Mon, Jul 18, 2011 at 1:20 AM, Senthil Kumar M
> <senthil.debian at gmail.com>wrote:
>
> > On Sun, Jul 17, 2011 at 3:58 PM, malvika sharan <malvikasharan at gmail.com
> >
> > wrote:
> > > 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.
> >
> > Hi,
> >
> > Could you please provide more details such as your operating system,
> > python/biopython versions and a minimal example of your script?
> >
> > On my system for example, 'from Bio.Blast.Applications import
> > NcbipsiblastCommandline' does not raise an error.
> >
> > senthil at deepthought ~ $ python
> > Python 2.6.6 (r266:84292, Sep 15 2010, 16:22:56)
> > [GCC 4.4.5] on linux2
> > Type "help", "copyright", "credits" or "license" for more information.
> > >>> import Bio
> > >>> print Bio.__version__
> > 1.57
> > >>> from Bio.Blast.Applications import NcbipsiblastCommandline
> > >>>
> >
> > senthil at deepthought ~ $ uname -srm
> > Linux 2.6.35-22-generic x86_64
> >
> > HTH
> >
> > Senthil
> >
> > -/
> > Time is an illusion, lunchtime doubly so.
> >                -- The Hitchhiker's Guide to the Galaxy
> >
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>