Menu
▾
▴
Re: [Gusdev-gusdev] Problem with GBParser
|
From: Thomas O. <ot...@fi...> - 2004-03-09 12:22:37
|
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
>>
>>
>
>
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by: IBM Linux Tutorials
> Free Linux tutorial presented by Daniel Robbins, President and CEO of
> GenToo technologies. Learn everything from fundamentals to system
> administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>
|
