[Bioperl-l] [GUSDEV] Another error executing ISF

Thu Jan 26 14:33:46 EST 2006

Sorry for the uninformative error message.

The unflattener uses a collection of heuristics to infer a canonical 
gene-mRNA-CDS-exon feature hierarchy from a flattened genbank style 
file. Due to the highly variable nature of some genbank records this 
isn't always possible, and some data massaging is required beforehand. 
I don't know what the context of this message is, but I presume you're 
aware of this from the docs.

The only time I've seen this before was with the genbank submission of 
the pombe genome, which has some very.. unusual features purportedly of 
type mRNA; the actual gene models are encoded using 'gene' and 'CDS' 
features. This confuses the heuristics a little. The only way I've been 
able to deal with this one was to manually remove the mRNA features 
(they appeared to be just fragments and not actual gene models) using 
$unf->remove_types(['mRNA']) beforehand.

Can you send the accession of the record you're trying this on (or 
email me the file off-list if it isn't too large). I'll try and get a 
more informative error message in there.

On Jan 26, 2006, at 10:19 AM, Ricardo Balbi wrote:

> Hi all,
>
>    Anybody could help me with this error ?
>
> thanks in advance,
> Ricardo
>
> 2006/1/26, Aaron J. Mackey <amackey at pcbi.upenn.edu>:
>>
>>
>> This is a BioPerl "Unflattener" error; it's unable to automatically
>> reconstruct the gene/mRNA/exon logic of some (or all) of the
>> annotation in your genbank file.  To get help with this, you should
>> post a message to the BioPerl mailing list (bioperl-l at bioperl.org),
>> including a snippet of your genbank file.
>>
>> -Aaron
>>
>> On Jan 26, 2006, at 11:53 AM, Ricardo Balbi wrote:
>>
>>> Hi all,
>>>
>>>   After making some changes in the gus mapping file to ignore some
>>> features of the kinetoplastida database, I followed in the
>>> execution of the ISF, however without success.
>>>
>>>   Somebody could help me with this error?
>>>
>>> thanks in advance,
>>> Ricardo
>>>
>>> ERROR:
>>>
>>> ------------- EXCEPTION  -------------
>>> MSG: structure_type 2 is currently unknown
>>> STACK Bio::SeqFeature::Tools::Unflattener::unflatten_seq /usr/local/
>>> bioperl15/Bio/SeqFeature/Tools/Unflattener.pm:1419
>>> STACK GUS::Supported::Plugin::InsertSequenceFeatures::unflatten /
>>> GUS/gus_home/lib/perl/GUS/Supported/Plugin/
>>> InsertSequenceFeatures.pm:353
>>> STACK
>>> GUS::Supported::Plugin::InsertSequenceFeatures::processFeatureTrees 
>>> /G
>>> US/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm:
>>> 720
>>> STACK GUS::Supported::Plugin::InsertSequenceFeatures::run /GUS/
>>> gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm:330
>>> STACK (eval) /GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm:
>>> 549
>>> STACK GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport /GUS/
>>> gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm:541
>>> STACK GUS::PluginMgr::GusApplication::doMajorMode_Run /GUS/gus_home/
>>> lib/perl/GUS/PluginMgr/GusApplication.pm:459
>>> STACK GUS::PluginMgr::GusApplication::doMajorMode /GUS/gus_home/lib/
>>> perl/GUS/PluginMgr/GusApplication.pm:357
>>> STACK GUS::PluginMgr::GusApplication::parseAndRun /GUS/gus_home/lib/
>>> perl/GUS/PluginMgr/GusApplication.pm:266
>>> STACK toplevel /GUS/gus_home/bin/ga:11
>>>
>>> --------------------------------------
>>>
>>> STACK TRACE:
>>>  at /usr/local/bioperl15/Bio/Root/Root.pm line 342
>>>         Bio::Root::Root::throw
>>> ('Bio::SeqFeature::Tools::Unflattener=HASH(0xb5e124c)',
>>> 'structure_type 2 is currently unknown') called at /usr/local/
>>> bioperl15/Bio/SeqFeature/Tools/Unflattener.pm line 1419
>>>         Bio::SeqFeature::Tools::Unflattener::unflatten_seq
>>> ('Bio::SeqFeature::Tools::Unflattener=HASH(0xb5e124c)', '-seq',
>>> 'Bio::Seq::RichSeq=HASH(0xb820b14)', '-use_magic', 1) called at /
>>> GUS/gus_home/lib/perl/GUS/Supported/Plugin/
>>> InsertSequenceFeatures.pm line 353
>>>         GUS::Supported::Plugin::InsertSequenceFeatures::unflatten
>>> ('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xa011adc)',
>>> 'Bio::Seq::RichSeq=HASH(0xb820b14)') called at /GUS/gus_home/lib/
>>> perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line 720
>>>
>>> GUS::Supported::Plugin::InsertSequenceFeatures::processFeatureTrees
>>> ('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xa011adc)',
>>> 'Bio::Seq::RichSeq=HASH(0xb820b14)', 140, 177) called at /GUS/
>>> gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
>>> line 330
>>>         GUS::Supported::Plugin::InsertSequenceFeatures::run
>>> ('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0xa011adc)',
>>> 'HASH(0xb047e98)') called at /GUS/gus_home/lib/perl/GUS/PluginMgr/
>>> GusApplication.pm line 549
>>>         eval {...} called at /GUS/gus_home/lib/perl/GUS/PluginMgr/
>>> GusApplication.pm line 541
>>>         GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport
>>> ('GUS::PluginMgr::GusApplication=HASH(0x9ff0c20)',
>>> 'GUS::Supported::Plugin::InsertSequenceFeatures', 1) called at /GUS/
>>> gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 459
>>>         GUS::PluginMgr::GusApplication::doMajorMode_Run
>>> ('GUS::PluginMgr::GusApplication=HASH(0x9ff0c20)',
>>> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at /GUS/
>>> gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 357
>>>         GUS::PluginMgr::GusApplication::doMajorMode
>>> ('GUS::PluginMgr::GusApplication=HASH(0x9ff0c20)',
>>> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at /GUS/
>>> gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 266
>>>         GUS::PluginMgr::GusApplication::parseAndRun
>>> ('GUS::PluginMgr::GusApplication=HASH(0x9ff0c20)', 'ARRAY
>>> (0xa004738)') called at /GUS/gus_home/bin/ga line 11
>>>
>>>
>>>
>>
>> --
>> Dr. Aaron J. Mackey, Ph.D.
>> Project Manager, ApiDB Bioinformatics Resource Center
>> Penn Genomics Institute, University of Pennsylvania
>> email:  amackey at pcbi.upenn.edu
>> office: 215-898-1205 (Biology, 212 Goddard Labs)
>>          215-746-7018 (PCBI, 1428 Blockley Hall)
>> fax:    215-746-6697 (Penn Genomics Institute)
>> postal: Penn Genomics Institute
>>          Goddard Labs 212
>>          415 S. University Avenue
>>          Philadelphia, PA  19104-6017
>>
>>
>>
>
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