[Biopython] PSI-BLAST

[malvika sharan]

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

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

its irrelevant with my programming cos the program dies at line 6.

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
>