[BioPython] PSI-Blast

[Jeffrey Chang]

Good catch!

blastpgp was using a functon called popen2.popen3 to call the blastpgp 
program.  The popen3 implementation for windows calls os.popen3, which 
didn't like that we passed in arguments as a list.  I've changed the 
code so that it now passes strings in instead, so the code should work 
on both windows and unix.  Please download the latest file:
biopython/Bio/Blast/NCBIStandalone.py

and install it over your old copy.  Let me know if there are still 
problems.
\
Jeff

On Wednesday, April 9, 2003, at 02:22  AM, Naveed Iqbal wrote:

> Hello,
>       Has anyone had any experience/success in running PSI-Blast
> locally? I used the code from the tutorial and it doesn't seem to work.
> I am running it on windows. I have the latest update of BioPython
> (1.10).
> Here is the code I have been trying to run.
> Any comments?
> ------------------------------------------------
> from Bio.Blast import *
> from sys import *
> file = "E:\\python22\\test.fa"
> blastexe = 'E:\\blast\\blastpgp.exe'
> database='E:\\blast\\prot'
>
> E_VALUE_THRESH = 0.04
>
> blast_out, error_info = NCBIStandalone.blastpgp(blastexe,database,file)
>
> b_parser = NCBIStandalone.PSIBlastParser()
> print "done"
> # this creates a Bio.Blast.Record.PSIBlast
> b_record = b_parser.parse(blast_out)
> ---------------------------------------------------
> Here is the error I get.
>
>   r, w, e = popen2.popen3([blastcmd] + params)
>   File "E:\Python22\lib\popen2.py", line 130, in popen3
>     w, r, e = os.popen3(cmd, mode, bufsize)
> TypeError: popen3() argument 1 must be string, not list
> ------------------------------------------------------
> Any help would be appreciated
>
>
> Naveed Iqbal
>
>
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