[BioPython] Problems with NCBIXML.py
Peter
biopython at maubp.freeserve.co.uk
Fri Oct 26 16:04:40 UTC 2007
Bruno Santos wrote:
> Peter Said:
>> Unless you want to keep the XML file for other analysis, it might be
>> simpler to parse the output from blast directly with Biopython -
>> avoiding having the large XML file on disk.
>
> But if even I don't want to save the results to an XML I still have to do
> the <blast_results = result_handle.read() #Catch the results> step right?
> And my problem is in this step not in writing to the file.
> Or I can use the result_handle directly, because I was reading the biopython
> documentation but it's not very clear.
The intention is something like this:
result_handle, error_handle = NCBIStandalone.blastall(my_blast_exe,
"blastn",my_blast_db, my_blast_file)
blast_records = NCBIXML.parse(result_handle)
for record in blast_records :
#do stuff
The bit about saving the results to a file and loading that to give a
new handle is optional, but very handy if you need to look at the raw
file by hand. Perhaps that section of the tutorial could be a little
clearer ...
Peter
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