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Re: [Gusdev-gusdev] Problem with GBParser
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From: Thomas O. <ot...@fi...> - 2004-03-08 20:37:10
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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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