[Bioperl-l] Reliability of get_Seq_by_gi

Wes Barris wes.barris at csiro.au
Mon Apr 5 23:09:51 EDT 2004

Rob Edwards wrote:

> Did you capture the errors and do they make any sense?

I did not capture any errors.  Usually, the message says that
the GI number does not exist although I know that it does.
I think that there are general reliability problems when getting
sequences from NCBI as there are when using netblast (blastcl3).

> Rob
> On Apr 5, 2004, at 5:44 PM, Wes Barris wrote:
>> Rob Edwards wrote:
>>> Just a suggestion, but have you tried making sure that $seq exists 
>>> before writing. Something like this should fix the problem:
> <snip>
>>> You should capture all the failed sequences and then validate them in 
>>> case there is some error with the Acc/GI (like they doesn't exist any 
>>> more).
>>> Rob
>> Hi Rob,
>> Your solution appears to have worked.  I was able to download sequences
>> over night and my script was still running this morning -- the first time
>> it has ever done that.  Thanks.

Wes Barris
E-Mail: Wes.Barris at csiro.au

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