[Biopython] PSI-BLAST

[malvika sharan]

please ignore the asterisk * , it appeared due to ctrl b.

On Mon, Jul 18, 2011 at 1:27 AM, malvika sharan <malvikasharan at gmail.com>wrote:

> 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
>>
>
>