[Biopython] PSI-BLAST

[Senthil Kumar M]

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

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