[Biopython-dev] [Bug 2480] Local BLAST fails: Spaces in Windows file-path values

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2480


biopython-bugzilla at maubp.freeserve.co.uk changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEW                         |RESOLVED
         Resolution|                            |FIXED




------- Comment #39 from biopython-bugzilla at maubp.freeserve.co.uk  2008-10-17 11:24 EST -------
(In reply to comment #37)
> Thank you. Confirming that CVS version 1.82 of the file works fine on Windows
> XP SP2 with Python 2.5.2.

Great - marking this bug as fixed.

> A note:
> 
>   A custom script using Bio/Blast can appear to hang, and the results file
> truncated, if the 'error handle' is used before the 'result handle':
> 
>   res_hdl, err_hdl = NCBIStandalone.blastall(my_blast, 'blastn', my_db, my_seq)
> 
>   # OK
>   my_result = res_hdl.read()
>   my_error = err_hdl.read()
> 
>   # Not OK
>   my_error = err_hdl.read()
>   my_result = res_hdl.read()

This is known and mentioned in the tutorial:
>> The error info can be hard to deal with, because if you try
>> to do a error_handle.read() and there was no error info
>> returned, then the read() call will block and not return,
>> locking your script. In my opinion, the best way to deal
>> with the error is only to print it out if you are not
>> getting result_handle results to be parsed, but otherwise
>> to leave it alone.

Thanks,

Peter


-- 
Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email
------- You are receiving this mail because: -------
You are the assignee for the bug, or are watching the assignee.