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Re: [Gusdev-gusdev] Problem with GBParser
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From: Steve F. <sfi...@pc...> - 2004-03-09 15:04:27
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Fantastic!
(don't worry about bothering us. go for it. sorry i didn't get to
your question before *you* did)
steve
Thomas Otto wrote:
> Problem solved - I rebuild all the perl objects with the
> generateGusObjects programm.
>
> Sorry for bothering you,
> Thomas
>
> Thomas Otto wrote:
>
>> Hi,
>>
>> I solved one problem, - I had a little problem with the source_row.pm
>> - I know I shouldn't have, (but I tried something).
>>
>> Anyhow, still doesn't work-
>> Errormessage now:
>> ------------------ entry number 1 -----------------
>> Error: attempting to access a child 'GUS::Model::DoTS::NALocation'
>> of table 'GUS::Model::DoTS::Source' , but that table does not have a
>> child of that type. at
>> /home/oracle/gus_home/lib/perl/GUS/Model/GusRow.pm line 396, <GEN0>
>> line 110.
>>
>> Thomas
>>
>> Thomas Otto wrote:
>>
>>> Hello,
>>>
>>> I have a little problem trying to insert a sequence from Genbank
>>> with the GBParser. (Errormessage and sequence-file (a cutted
>>> version) see below!)
>>>
>>> Looks like, that the table doesn't exists! Do I have to create the
>>> table or is the GBParser not able to insert this type of entries in
>>> general.
>>>
>>> I will continue to resolve the problem, but maybe someone might help
>>> me.
>>>
>>> Thanks a lot,
>>> Thomas
>>>
>>>
>>> Error msg:
>>> Invalid child name: 'GUS::Model::DoTS::AAFeatureComment' at
>>> /home/oracle/gus_home/lib/perl/GUS/ObjRelP/DbiTable.pm line
>>> 851
>>> GUS::ObjRelP::DbiTable::addToChildList('GUS::Model::DoTS::Source_Table=HASH(0x8fc9b44)','ARRAY(0x8fee070)','ARRAY(0x8fee0ac)','ARRAY(0x8fee0e8)','ARRAY(0x8fee124)','ARRAY(0x8fee160)','ARRAY(0x8fee19c)','ARRAY(0x8fee1d8)','ARRAY(0x8fee214)',...)
>>> called at /home/oracle/gus_home/lib/perl/GUS/ObjRelP/DbiTable.pm
>>> line 844
>>>
>>> GUS::ObjRelP::DbiTable::setChildList('GUS::Model::DoTS::Source_Table=HASH(0x8fc9b44)','ARRAY(0x8fee070)','ARRAY(0x8fee0ac)','ARRAY(0x8fee0e8)','ARRAY(0x8fee124)','ARRAY(0x8fee160)','ARRAY(0x8fee19c)','ARRAY(0x8fee1d8)','ARRAY(0x8fee214)',...)
>>> called at
>>> /home/oracle/gus_home/lib/perl/GUS/Model/DoTS/Source_Table.pm line 16
>>>
>>> GUS::Model::DoTS::Source_Table::setDefaultParams('GUS::Model::DoTS::Source_Table=HASH(0x8fc9b44)')
>>> called at /home/oracle/gus_home/lib/perl/GUS/ObjRelP/DbiTable.pm
>>> line 38
>>>
>>> GUS::ObjRelP::DbiTable::new('GUS::Model::DoTS::Source_Table','GUS::Model::DoTS::Source','GUS::ObjRelP::DbiDatabase=HASH(0x8c0e34c)')
>>> called at /home/oracle/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm
>>> line 179
>>>
>>> GUS::ObjRelP::DbiDatabase::getTable('GUS::ObjRelP::DbiDatabase=HASH(0x8c0e34c)','GUS::Model::DoTS::Source')
>>> called
>>> at /home/oracle/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 30
>>>
>>> GUS::ObjRelP::DbiRow::new('GUS::ObjRelP::DbiRow','GUS::Model::DoTS::Source','HASH(0x8fcb890)','undef','undef')
>>> called at /home/oracle/gus_home/lib/perl/GUS/Model/GusRow.pm line 25
>>>
>>> GUS::Model::GusRow::new('GUS::Model::DoTS::Source','HASH(0x8fcb890)')
>>> called at
>>> /home/oracle/gus_home/lib/perl/GUS/Common/Plugin/GBParser.pm line 486
>>>
>>> GUS::Common::Plugin::GBParser::buildFeatures('GUS::Common::Plugin::GBParser=HASH(0x856fbac)','CBIL::Bio::GenBank::Entry=HASH(0x8ec70f4)','GUS::Model::DoTS::ExternalNASequence=HASH(0x8f95ea8)')
>>> called at
>>> /home/oracle/gus_home/lib/perl/GUS/Common/Plugin/GBParser.pm line 251
>>>
>>> GUS::Common::Plugin::GBParser::processEntry('GUS::Common::Plugin::GBParser=HASH(0x856fbac)','CBIL::Bio::GenBank::ArrayStream=HASH(0x8ec7088)')
>>> called at
>>> /home/oracle/gus_home/lib/perl/GUS/Common/Plugin/GBParser.pm line 185
>>> eval {...} called at
>>> /home/oracle/gus_home/lib/perl/GUS/Common/Plugin/GBParser.pm line 184
>>>
>>> GUS::Common::Plugin::GBParser::run('GUS::Common::Plugin::GBParser=HASH(0x856fbac)','HASH(0x8e53714)')
>>> called at
>>> /home/oracle/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 430
>>> eval {...} called at
>>> /home/oracle/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 427
>>>
>>> GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x804d00c)','GUS::Common::Plugin::GBParser')
>>> called at
>>> /home/oracle/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 283
>>>
>>> GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x804d00c)','GUS::Common::Plugin::GBParser')
>>> called at
>>> /home/oracle/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 192
>>>
>>> GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x804d00c)','ARRAY(0x80606b0)')
>>> called at /home/oracle/gus_home/bin/ga line 11
>>>
>>> ------------------------------------------------------------------------
>>>
>>> LOCUS ATT8B10 103787 bp DNA linear PLN
>>> 20-MAR-2000
>>> DEFINITION Arabidopsis thaliana DNA chromosome 3, BAC clone T8B10.
>>> ACCESSION AL138646
>>> VERSION AL138646.2 GI:7287982
>>> KEYWORDS .
>>> SOURCE Arabidopsis thaliana (thale cress)
>>> ORGANISM Arabidopsis thaliana
>>> Eukaryota; Viridiplantae; Streptophyta; Embryophyta;
>>> Tracheophyta;
>>> Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots;
>>> rosids; eurosids II; Brassicales; Brassicaceae; Arabidopsis.
>>> REFERENCE 1 (bases 1 to 103787)
>>> AUTHORS Rieger,M., Mueller-Auer,S., Zipp,M., Schaefer,M.,
>>> Mewes,H.W.,
>>> Lemcke,K., Mayer,K.F.X., Quetier,F. and Salanoubat,M.
>>> JOURNAL Unpublished
>>> REFERENCE 2 (bases 1 to 103787)
>>> AUTHORS EU Arabidopsis sequencing,project.
>>> TITLE Direct Submission
>>> JOURNAL Submitted (20-MAR-2000) MIPS, at the Max-Planck-Institut
>>> fuer
>>> Biochemie, Am Klopferspitz 18a, D-82152 Martinsried, FRG,
>>> E-mail:
>>> le...@mi...,ma...@mi... Project
>>> Coordinator: Marcel Salanoubat and Francis Quetier,
>>> Groupement
>>> d'Interet Public, Centre National de Sequencage -
>>> GENOSCOPE; 2 rue
>>> Gaston Cremieux, BP191, 91006 Evry Cedex, France;
>>> http://www.genoscope.cns.fr
>>> FEATURES Location/Qualifiers
>>> source 1..103787
>>> /organism="Arabidopsis thaliana"
>>> /mol_type="genomic DNA"
>>> /variety="Columbia"
>>> /db_xref="taxon:3702"
>>> /chromosome="3"
>>> gene 8353..12143
>>> /gene="T8B10_10"
>>> gene complement(join(8353..8556,8641..8947,9034..9209,
>>> 9288..9351,9485..9579,9673..9888,10013..10144,
>>> 10459..10539,10632..12143))
>>> /gene="T8B10_10"
>>> CDS complement(join(8353..8556,8641..8947,9034..9209,
>>> 9288..9351,9485..9579,9673..9888,10013..10144,
>>> 10459..10539,10632..12143))
>>> /gene="T8B10_10"
>>> /note="similarity to arm repeat containing protein
>>> homolog, Arabidopsis thaliana, EMBL:AL133314"
>>> /codon_start=1
>>> /product="Arm repeat containing protein-like"
>>> /protein_id="CAB81821.1"
>>> /db_xref="GI:7287983"
>>> /db_xref="TrEMBL:Q9M224"
>>>
>>> /translation="MSRRVRQRVEDNGKYKVDSPSYTVIGVEDLAPKVQQYVNWTSLP
>>>
>>> YDTVFHLFTRLNYRDRASLASTCRTWRSLGASSFLWSSLDLRAHKFDLSMAASLATRC
>>>
>>> VDLQKIRFRGVDSADAIIHLKARSLLEISGDYCRKITDATLSMIAARHEALESLQLGP
>>>
>>> DFCERITSDAIRVIAFCCPKLKKLRVSGMRDVSSEAIESLAKHCPQLSDLGFLDCLNI
>>>
>>> NEEALGKVVSLRYLSVAGTSNIKWKVALENWEKLPKLIGLDVSRTTIDHIAVSRLLKS
>>>
>>> SQSLKVLCALNCPYLEEDKSYSSNRFKGKVLLAVFTDTFDELASIFADNSKKPKNIFS
>>>
>>> YWRDLIRKDKSIDEIMLWIEWIISHTLLRIAESSNSQGLNDFWLNQGATLLLSLMQSA
>>>
>>> QEDVQERAATGLATFIVVDDENASIDCGRAEAVMRDGGIRLLLELAKSWREGLQSEAA
>>>
>>> KAIANLSVNAKVAKAVAEEGGISVLADLAKSMNRLVAEEAAGGLWNLSVGEEHKNAIA
>>>
>>> QAGGVNALVDLIFRWPHGCDGVLERAAGALANLAADDKCSMEVARAGGVHALVMLARN
>>>
>>> CKYEGAQEQAARALANLAAHGDSNGNNAAVGQEAGALEALVQLTQSPHEGVKQEAAGA
>>>
>>> LWNLAFDDKNRESIAAFGGVEALVALAKSSSNASTGLQERVAGALWGLSVSEANSIAI
>>>
>>> GHEGGIPPLIALVRSEAEDVHETAAGALWNLSFNPGNALRIVEEGGVVALVQLCSSSV
>>>
>>> SKMARFMAALALAYMFDGRMDEYAMIGTSLESTSKSVTLNGARTMALDQIKAFIKTFM
>>>
>>> EHQIFSTGALSSAPSMLAQVSERARIPEAGHLRCSGSEIGRFVTMLRNPCLVLRACAA
>>>
>>> FALLQFTIPESRHAMHHASLMQNAGEARGLRSAAAAASMPREAKIFMKIVLRNLEHQQ
>>> AESPEGMKVSYNRI"
>>> exon complement(8353..8556)
>>> /gene="T8B10_10"
>>> /number=1
>>> intron complement(8557..8640)
>>> /gene="T8B10_10"
>>> /number=1
>>> exon complement(8641..8947)
>>> /gene="T8B10_10"
>>> /number=2
>>> intron complement(8948..9033)
>>> /gene="T8B10_10"
>>> /number=2
>>> exon complement(9034..9209)
>>> /gene="T8B10_10"
>>> /number=3
>>> intron complement(9210..9287)
>>> /gene="T8B10_10"
>>> /number=3
>>> exon complement(9288..9351)
>>> /gene="T8B10_10"
>>> /number=4
>>> intron complement(9352..9484)
>>> /gene="T8B10_10"
>>> /number=4
>>> exon complement(9485..9579)
>>> /gene="T8B10_10"
>>> /number=5
>>> intron complement(9580..9672)
>>> /gene="T8B10_10"
>>> /number=5
>>> exon complement(9673..9888)
>>> /gene="T8B10_10"
>>> /number=6
>>> intron complement(9889..10012)
>>> /gene="T8B10_10"
>>> /number=6
>>> exon complement(10013..10144)
>>> /gene="T8B10_10"
>>> /number=7
>>> intron complement(10145..10458)
>>> /gene="T8B10_10"
>>> /number=7
>>> exon complement(10459..10539)
>>> /gene="T8B10_10"
>>> /number=8
>>> intron complement(10540..10631)
>>> /gene="T8B10_10"
>>> /number=8
>>> exon complement(10632..12143)
>>> /gene="T8B10_10"
>>> /number=9
>>> ORIGIN 1 aagctttgaa gggctaacgg gtgatgcttt ggtgaaggtt
>>> ttttctggtc caggtttgtg
>>> 61 cttattttgc attgcttctc tttgattcac gtctgcataa acatcaaata
>>> attcatttat
>>> 121 gtttgagttg attatgtaga aaaaattatt aggggagatg ctttatgata
>>> agaaaaaaaa
>>> 181 gtggtcttgt ggtatcttaa ggcagaagga aaatatttag tgtcttaatg
>>> agtaatagat
>>> 241 ttatctgtct atccagattt tataactgag ttttagtaac ttccggctca
>>> agcaaaaagg
>>> 301 aagttcgata tgacggacat agaagctctc aaggctatca ccacggagag
>>> cattgatctg
>>> 361 gtatgtactt ttatacctca ccactttttt tttgcagatg attgcttctg
>>> atagctttta
>>>
>>>
>>
>>
>>
>>
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>
>
>
>
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