[Biopython] PSI-BLAST

[malvika sharan]

Thank you Peter and Eric.

you are right and i think i should have known this :(
I updated Biopython. and revising my codes. it should work now.

Malvika

On Tue, Jul 19, 2011 at 8:08 AM, Peter Cock <p.j.a.cock at googlemail.com>wrote:

> On Monday, July 18, 2011, Eric Talevich <eric.talevich at gmail.com> wrote:
> > 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.
> >
>
> Correct. The BLAST+ wrappers were added in Biopython 1.53.
> You will need to update it, ideally to the current release, 1.57
>
> In general if some imports work and others fail, your library
> Is either too old (and what you want didn't exist in the old
> version), or too new (the code you want to use was obsolete
> and removed).
>
> Peter
>