[Bioperl-l] Extracting gi no from refseq record

[Hilmar Lapp]

On Thursday, April 3, 2003, at 07:20  AM, Jason Stajich wrote:

> we only pick up GI from
> the field here, I assume the file in question has this line?
>
> I notice we don't try and parse NID lines from Genbank.
>
> VERSION     AI129902.1  GI:3598416
>

RefSeq does feature this line, at least the last time I checked. We 
also do test for this being parsed correctly, namely in t/SeqIO.t. It's 
not always as bad as it sometimes seems. I ran an entire download of 
RefSeq a couple weeks ago and the GI# was parsed out of every single 
record.

Siddharta, do you run at least bioperl 1.2? If you do, can you run

	$ make test_SeqIO

from the root directory of the bioperl distribution? Can you please 
mail the output? If a test fails, could you please run

	$ make test_SeqIO TEST_VERBOSE=1

and mail the output for the failed test(s)?

If no test fails, could you email the accession# of the sequence you 
retrieved and for which there was no GI#?

	-hilmar

-- 
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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