[Biopython-dev] python newbies blast problem

h.j.tipney at stud.man.ac.uk h.j.tipney at stud.man.ac.uk
Tue Jul 13 09:56:43 EDT 2004

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 
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 
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 

    from Bio import Fasta
    from Bio.Blast import NCBIWWW
    import sys
    import getopt

    opts, args =

    print sys.argv
    print opts

    if len(args)==0:
        print "no file given"

    program = "blastn"
    database = "nr"
    format = "Text"
    #"Homo sapiens [ORGN]"


    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]"

    print "program = %s , database = %s, query = %s" %

    file_for_blast = open(args[0], 'r')
    f_iterator = Fasta.Iterator(file_for_blast)

    f_record = f_iterator.next()
    b_results = NCBIWWW.blast(program, database,
    f_record,format_type=format, entrez_query=query,timeout=60)

    blast_results = b_results.read()

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

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

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