Re: [Gusdev-gusdev] GBParser bug

[Jonathan S. <js...@pc...>]

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
>>
>>
>>
>> -------------------------------------------------------
>> This SF.Net email is sponsored by: SourceForge.net Broadband
>> Sign-up now for SourceForge Broadband and get the fastest
>> 6.0/768 connection for only $19.95/mo for the first 3 months!
>> http://ads.osdn.com/?ad_id=2562&alloc_id=6184&op=click
>> _______________________________________________
>> Gusdev-gusdev mailing list
>> Gus...@li...
>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>
>>
Jonathan Schug  -   js...@pc...