Re: [Gusdev-gusdev] GBParser bug

[Fidel S. <fi...@vb...>]

Jonathan,

Hi!

We do not have access to CBIL's source tree except through compressed
tar files.  The most recent file available is from 5/6/2004 and
therefore it does not contain your edits.

Fidel


Jonathan Schug <js...@pc...> writes:

     > Hi Fidel!
>
     > I believe I have fixed this error.  I have committed files in
     > CBIL/Bio/lib/perl/GenBank that contain the changes.
>
     > Please let me know if it is working now.
>
     > Thanks,
>
     > Jonathan
>
     > On May 18, 2004, at 9:32 AM, Angel Pizarro wrote:
>
>> Fidel Salas wrote:
>>
>>> There is a bug in the parser that only becomes expressed if the DNA
>>> sequence goes over 99999999 nucleotides.  An error gets output like
>>> this:
>>> ERR     LINE=2575409    unparsed line   100000021 cggggcgggg
>>> agactaggag aaagctgcca gaggctgctg gcaagagata tccactggtt
>>>
>>>
>> Fidel, I suspect that this error is coming from the support gbff
>> parser CBIL::GenBank modules. J. Schug is the author and I'll ask
>> him if he knows what causes this.
>>
>> Angel
>>
>>> The error happens because the parser assumes that there will be spaces
>>> before the number indicating the nucleotide number.  That is the case
>>> until the number of nucleotides goes over the threshold value
>>> indicated above.
>>>
>>> Fidel
>>>
>>>
>>>
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     > Jonathan Schug  -   js...@pc...