[BioPython] said Your XML file was empty in parsing blast records but can see the results in the saved xml file
Hongwu Ma
hma2 at staffmail.ed.ac.uk
Thu Nov 13 11:18:34 UTC 2008
Sometimes when I parse the blast records in biopython using the
following program I get the error "Your XML file was empty" but there
are actually some results in the saved xml files. Anyone know what is
the problem?
Thanks in advance.
Hongwu
myfolder='c:/mgenome/'
mydatafolder=myfolder+'alphao/'
my_blast_db = myfolder+'orfsre.txt'
my_blast_exe =myfolder+'blastall.exe'
evalue=0.0001
my_blast_file = mydatafolder+file
result_handle, error_handle =
NCBIStandalone.blastall(blastcmd=my_blast_exe,
program="tblastn",
database=my_blast_db,
infile=my_blast_file,
expectation=evalue)
bres=result_handle.read()
save_file = open(myfolder+file[:3]+'orfre.xml', "w")
save_file.write(bres)
save_file.close()
blast_records = NCBIXML.parse(result_handle)
for blast_record in blast_records:
>
>
>
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