[BioPython] python newbies blast problem

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

Hi
I'm hoping someone 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=','entrez_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)

------------------------------------------
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