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

[Frank Kauff]

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