[BioPython] parsing the blastoutput and printing the alingment

[Peter]

Muthuraman, Manickam wrote:
> Still i am getting the same error or error. I tried as Peter suggested but it fails. 
 > ...

I couldn't see anything clearly wrong just from reading your code.

Which version of BioPython do you have?

Since BioPython 1.41 NCBIWWW.qblast uses XML as the default output 
format, but you can force this by:

result_handle=NCBIWWW.qblast('blastp','nr',f_record, format_type="XML")

Try opening your output file /home/manickam/my_blast.out in a text 
editor to double check it really is XML - i.e. does it start <XML...>

If it is XML, then BioPython doesn't like it for some reason.  Maybe you 
could email the file to me and Michiel to take a look?

Peter