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Re: [GUSDEV] ISF error in loading influenza sequence
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From: Ed R. <ero...@ug...> - 2006-07-10 14:38:48
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The GB record lacks a gene feature but has mRNA and CDS features. The Unflattener, as it operates in ISF, infers a feature hierarchy. It can add mRNA and CDS records, but it assumes the existence of a gene feature. Since the file doesn't supply a gene feature, the Unflattener cannot build a valid hierarchy.
How many files do you have like this? You can easily modify ISF to build different hierarchies, but the Unflattener always requires an explicit gene feature to start its hierachy. If you have a bunch of files, I would recommend writting a pre-parser to add gene features everytime you find a gene-less mRNA record. A simple BioPerl In and Out script with a conditional to add the gene feature to the std out every time you find an mRNA feature should do the trick.
-ed
---- Original message ----
>Date: Fri, 7 Jul 2006 18:02:23 -0400
>From: "Kumar, Sanjeev" <San...@ng...>
>Subject: Re: [GUSDEV] ISF error in loading influenza sequence
>To: "Steve Fischer" <sfi...@pc...>
>Cc: gus...@li...
>
>Hi Steve,
> The file is small genBank file. Let me attach the file.
> And the command I am using to load is as follows:
>ga GUS::Supported::Plugin::InsertSequenceFeatures --seqFile $loadFile
>--mapFile /home/oragus35/genbank2gus.xml --fileFormat 'genbank'
>--extDbName $database --extDbRlsVer $dbVersion --soCvsVersion 3354
>--gusconfigfile /home/oragus35/GUS/gus.properties --commit
>2>>$outputFile`;
>
>Thanks
>Sanjeev
>
>
>-----Original Message-----
>From: Steve Fischer [mailto:sfi...@pc...]
>Sent: Friday, July 07, 2006 5:54 PM
>To: Kumar, Sanjeev
>Cc: gus...@li...
>Subject: Re: [GUSDEV] ISF error in loading influenza sequence
>
>sanjeev-
>
>how big is the file you are trying to load? i want to take a look at
>it. is it in genbank? what is its accession?
>
>can you send the command line?
>
>
>steve
>
>Kumar, Sanjeev wrote:
>> Hi Group,
>> I am getting following error when I am trying to load one
>> influenza sequence using "InsertSequenceFeature' plugin.
>> I am not able to figure out the reason of the failure. I need your
>
>> assistance, any help will be appreciated.
>> The sequence file is attached.
>>
>>
>> Thanks
>> Sanjeev Kumar
>> Northrop Grumman
>>
>> ERROR:
>>
>> ------------- EXCEPTION -------------
>> *MSG: structure_type 2 is currently unknown
>> *STACK Bio::SeqFeature::Tools::Unflattener::unflatten_seq
>>
>/home/oragus35/perl/lib/site_perl/5.8.7/Bio/SeqFeature/Tools/Unflattener
>.pm:1419
>> STACK GUS::Supported::Plugin::InsertSequenceFeatures::unflatten
>>
>/home/oragus35/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequence
>Features.pm:383
>> STACK GUS::Supported::Plugin::InsertSequenceFeatures::run
>>
>/home/oragus35/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequence
>Features.pm:358
>> STACK (eval)
>>
>/home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm:469
>> STACK GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport
>>
>/home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm:461
>> STACK GUS::PluginMgr::GusApplication::doMajorMode_Run
>>
>/home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm:380
>> STACK GUS::PluginMgr::GusApplication::doMajorMode
>>
>/home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm:288
>> STACK GUS::PluginMgr::GusApplication::parseAndRun
>>
>/home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm:197
>> STACK toplevel /home/oragus35/GUS/gus_home/bin/ga:11
>> --------------------------------------
>> STACK TRACE:
>> at /home/oragus35/perl/lib/site_perl/5.8.7/Bio/Root/Root.pm line
>> 342
>>
>>
>Bio::Root::Root::throw('Bio::SeqFeature::Tools::Unflattener=HASH(0xa237d
>08)',
>> 'structure_type 2 is currently unknown') called at
>>
>/home/oragus35/perl/lib/site_perl/5.8.7/Bio/SeqFeature/Tools/Unflattener
>.pm
>> line 1419
>>
>>
>Bio::SeqFeature::Tools::Unflattener::unflatten_seq('Bio::SeqFeature::Too
>ls::Unflattener=HASH(0xa237d08)',
>> '-seq', 'Bio::Seq::RichSeq=HASH(0x9febe2c)', '-use_magic', 1)
>> called at
>>
>/home/oragus35/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequence
>Features.pm
>> line 383
>>
>>
>GUS::Supported::Plugin::InsertSequenceFeatures::unflatten('GUS::Supporte
>d::Plugin::InsertSequenceFeatures=HASH(0x9414bf0)',
>> 'Bio::Seq::RichSeq=HASH(0x9febe2c)') called at
>>
>/home/oragus35/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequence
>Features.pm
>> line 358
>>
>>
>GUS::Supported::Plugin::InsertSequenceFeatures::run('GUS::Supported::Plu
>gin::InsertSequenceFeatures=HASH(0x9414bf0)',
>> 'HASH(0x9ef7284)') called at
>>
>/home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>> line 469
>> eval {...} called at
>>
>/home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>> line 461
>>
>>
>GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr:
>:GusApplication=HASH(0x8f74180)',
>> 'GUS::Supported::Plugin::InsertSequenceFeatures', 1) called at
>>
>/home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>> line 380
>>
>>
>GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusAppl
>ication=HASH(0x8f74180)',
>> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at
>>
>/home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>> line 288
>>
>>
>GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplicat
>ion=HASH(0x8f74180)',
>> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at
>>
>/home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>> line 197
>>
>>
>GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplicat
>ion=HASH(0x8f74180)',
>> 'ARRAY(0x8f74924)') called at /home/oragus35/GUS/gus_home/bin/ga
>> line 11
>>
>>
>>
>>
>> ----------------------------------------------------------------------
>> --
>>
>> Using Tomcat but need to do more? Need to support web services,
>security?
>> Get stuff done quickly with pre-integrated technology to make your job
>
>> easier Download IBM WebSphere Application Server v.1.0.1 based on
>> Apache Geronimo
>> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=1216
>> 42
>> ----------------------------------------------------------------------
>> --
>>
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>>
>________________
>FLBHAOA.gbf (8k bytes)
>________________
>Using Tomcat but need to do more? Need to support web services, security?
>Get stuff done quickly with pre-integrated technology to make your job easier
>Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
>http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
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-----------------
Ed Robinson
Center for Tropical and Emerging Global Diseases
University of Georgia, Athens, GA 30602
ero...@ug.../(706)542.1447/254.8883
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