[Bioperl-l] Hierarchical location parsing

Brian Osborne brian_osborne at cognia.com
Fri Mar 25 11:52:46 EST 2005


Can you also attach the sequence file that you used in order to test your
code? That way I can write a test specifically for the parsing of
hierarchical locations.

You wrote "I'm not sure the new patch won't slow down location parsing
considerably..." Have you actually timed the parsing using the old and new

Thanks again,

Brian O.

-----Original Message-----
From: Mark Hoebeke [mailto:Mark.Hoebeke at jouy.inra.fr]
Sent: Friday, March 25, 2005 10:57 AM
To: brian.osborne at cognia.com
Cc: bioperl-l at portal.open-bio.org
Subject: Re: [Bioperl-l] Hierarchical location parsing

Hi Brian,

In fact, I filed a bug request (#1765) to which I attached a patch.

I checked that the patched FTLocationFactory.pm and the unpatched one in
the bioperl-live CVS repository exposed the same behaviour when running
'make test'.

Of course, I don't know the variety of location descriptions found in
the test scripts...


> Mark,
> I'm afraid I don't know the answer to your question but let me turn the
> question around: would you like to help us fix this?
> Brian O.
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