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From: Fidel S. <fi...@vb...> - 2004-05-17 21:41:20
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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 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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From: Steve F. <sfi...@pc...> - 2004-05-17 21:55:55
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Thanks Fidel. Do you have a suggested patch? steve 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 > >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 > > |
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From: Fidel S. <fi...@vb...> - 2004-05-17 21:59:52
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Steve,
Sorry, I do not have a suggested patch at this moment.
Fidel
Steve Fischer <sfi...@pc...> writes:
> Thanks Fidel. Do you have a suggested patch?
>
> steve
>
> 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
>>
>>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
>>
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From: Angel P. <an...@pc...> - 2004-05-18 13:32:53
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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 > > |
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From: Jonathan S. <js...@pc...> - 2004-05-18 20:12:41
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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... |
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From: Fidel S. <fi...@vb...> - 2004-05-19 05:36:38
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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
>>>
>>>
>>>
>>> -------------------------------------------------------
>>> 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...
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From: Steve F. <st...@pc...> - 2004-05-19 11:57:26
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i will make a new .tar today. in the meantime, jonathan, if its is one file, can you email it? steve 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 >>>> >>>> >>>> >>>>------------------------------------------------------- >>>>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... > > > >------------------------------------------------------- >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 > > |
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From: Jonathan S. <js...@pc...> - 2004-05-20 05:25:31
Attachments:
Entry.pm
Sequence.pm
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Fidel: Here are the relevant files. They belong at this path: Projects/CBIL/Bio/lib/perl/GenBank Let me know they work. Jonathan |
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From: Fidel S. <fi...@vb...> - 2004-05-21 03:50:59
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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
>>>>>
>>>>>
>>>>>
>>>>> -------------------------------------------------------
>>>>> 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...
|
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