[Biopython-dev] python newbies blast problem

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

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