[Biopython] PSI-BLAST

[Peter Cock]

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