Re: [Gusdev-gusdev] GBParser bug

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

Jonathan,

Thanks!  They work.

Fidel


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

     > Fidel:
>
     > Here are the relevant files.  They belong at this path:
>
     > Projects/CBIL/Bio/lib/perl/GenBank
>
     > Let me know they work.
>
     > Jonathan
>
>
>
>
>
>
     > On May 19, 2004, at 1:29 AM, Fidel Salas wrote:
>
>> 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...