[BioPython] Re: [Biopython-dev] python newbies blast problem

[h.j.tipney at stud.man.ac.uk]

Thank you all for your help - my scripts are all up and running again 
now - phew!
Cheers
Hannah

Subject:        	Re: [Biopython-dev] python newbies blast problem
From:           	Frank Kauff <fkauff at duke.edu>
To:             	biopython at biopython.org
Organization:   	Duke University
Date sent:      	Thu, 15 Jul 2004 09:51:11 -0400

> Thanks, Jeff! It woorks fine with my scripts.
> 
> Frank
> 
> On Tue, 2004-07-13 at 23:47, Jeffrey Chang wrote:
> > Hello,
> > 
> > This is because the NCBI website is not really meant to be queried
> > by computer scripts.  It looks like a recent change has broken the
> > NCBIWWW.blast function.  Fortunately, NCBI does have a computer
> > friendly BLAST API called QBLAST.  I added an interface to QBLAST
> > into biopython called NCBIWWW.qblast.  Please get the updated
> > version of the NCBIWWW.py from CVS, and replace NCBIWWW.blast with
> > NCBIWWW.qblast in your script, and see if that fixes things.
> > 
> > The anonymous CVS is at:
> > http://cvs.biopython.org/
> > 
> > Jeff
> > 
> > 
> > 
> > 
> > On Jul 13, 2004, at 9:56 AM, h.j.tipney at stud.man.ac.uk wrote:
> > 
> > > Hi
> > > I posted this to the other mailing list and got no response so I'm
> > > hoping you guys can help me. I'm very new to programming and even
> > > newer to python, so I apologise in advance if this is a simple
> > > problem with an obvious solution but there are no python
> > > programmers near to help me. Anyway, I inherited the script below
> > > and have been using it on and off as part of a larger workflow. It
> > > has been running fine, but I ran it again last week and it didn't
> > > give the output I expected - it returned the 'your results will be
> > > updated in X seconds' page rather than the actual results. It has
> > > been a while since I had used this program and both blast and
> > > biopython had been updated so I've now got the new biopython
> > > release (1.30) but I still get the 'wrong' output. I'm using
> > > python 2.3.3 on solaris, if that helps. Any help would be greatly
> > > appreciated! Thank you in advance Hannah Tipney
> > >
> > >     #!/opt/cs/bin/python
> > >     from Bio import Fasta
> > >     from Bio.Blast import NCBIWWW
> > >     import sys
> > >     import getopt
> > >
> > >     opts, args =
> > >     getopt.getopt(sys.argv[1:],"",['program=','database=','format=
> > >     ','e ntrez_query='])
> > >
> > >     print sys.argv
> > >     print opts
> > >
> > >     if len(args)==0:
> > >         print "no file given"
> > >         sys.exit(2)
> > >
> > >     program = "blastn"
> > >     database = "nr"
> > >     format = "Text"
> > >     #"Homo sapiens [ORGN]"
> > >
> > >     short_query=""
> > >
> > >     for o,a in opts:
> > >         print o,a
> > >         if o == "--program":
> > >             program = a
> > >         if o == "--database":
> > >             database = a
> > >         if o == "--format":
> > >             format = a
> > >         if o == "--entrez_query":
> > >      short_query = a
> > >
> > >     if short_query=="human":
> > >         query="Homo sapiens [ORGN]"
> > >     else:
> > >         query=""
> > >
> > >     print "program = %s , database = %s, query = %s" %
> > >     (program,database,query)
> > >
> > >     file_for_blast = open(args[0], 'r')
> > >     f_iterator = Fasta.Iterator(file_for_blast)
> > >
> > >     f_record = f_iterator.next()
> > >     file_for_blast.close()
> > >     b_results = NCBIWWW.blast(program, database,
> > >     f_record,format_type=format, entrez_query=query,timeout=60)
> > >
> > >     blast_results = b_results.read()
> > >     sys.stdout.write(blast_results)
> > >
> > > ------- End of forwarded message -------
> > > ------------------------------------------
> > > Hannah Tipney
> > > Manchester University,
> > > Academic Unit of Medical Genetics,
> > > St Mary's Hospital,
> > > Hathersage Road,
> > > Manchester. M13 0JH.
> > > UK
> > >
> > > tel: +44 (0)161 276 6602
> > > fax: +44 (0)161 276 6606
> > > _______________________________________________
> > > Biopython-dev mailing list
> > > Biopython-dev at biopython.org
> > > http://biopython.org/mailman/listinfo/biopython-dev
> > 
> > _______________________________________________
> > Biopython-dev mailing list
> > Biopython-dev at biopython.org
> > http://biopython.org/mailman/listinfo/biopython-dev
> -- 
> Frank Kauff
> Dept. of Biology
> Duke University
> Box 90338
> Durham, NC 27708
> USA
> 
> Phone 919-660-7382
> Fax 919-660-7293
> Web http://www.lutzonilab.net/member/frankkauff.shtml
> 


------------------------------------------
Hannah Tipney
Manchester University,
Academic Unit of Medical Genetics,
St Mary's Hospital,
Hathersage Road,
Manchester. M13 0JH. 
UK

tel: +44 (0)161 276 6602
fax: +44 (0)161 276 6606