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<p class="MsoNormal">Hi,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I am attempting to load 3 gff3 files into a postgres Bio::DB::SeqFeature::Store database using the bp_seqfeature_load.pl script that comes with bioperl.<o:p></o:p></p>
<p class="MsoNormal">My files are: chromosomes.gff3, ideogram.gff3 and study_2.gff3, being loaded in that order. The chromosomes.gff3 file loads without error. However, when I attempt to load either of the other 2 files, I receive the following error:<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">------------- EXCEPTION: Bio::Root::Exception -------------<o:p></o:p></p>
<p class="MsoNormal">MSG: chr1 doesn't have a primary id<o:p></o:p></p>
<p class="MsoNormal">STACK: Error::throw<o:p></o:p></p>
<p class="MsoNormal">STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:472<o:p></o:p></p>
<p class="MsoNormal">STACK: Bio::DB::SeqFeature::Store::GFF3Loader::build_object_tree_in_tables /usr/lib/perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store/GFF3Loader.pm:720<o:p></o:p></p>
<p class="MsoNormal">STACK: Bio::DB::SeqFeature::Store::GFF3Loader::build_object_tree /usr/lib/perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store/GFF3Loader.pm:699<o:p></o:p></p>
<p class="MsoNormal">STACK: Bio::DB::SeqFeature::Store::GFF3Loader::finish_load /usr/lib/perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store/GFF3Loader.pm:343<o:p></o:p></p>
<p class="MsoNormal">STACK: Bio::DB::SeqFeature::Store::Loader::load_fh /usr/lib/perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store/Loader.pm:354<o:p></o:p></p>
<p class="MsoNormal">STACK: Bio::DB::SeqFeature::Store::Loader::load /usr/lib/perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store/Loader.pm:243<o:p></o:p></p>
<p class="MsoNormal">STACK: /usr/bin/bp_seqfeature_load.pl:135<o:p></o:p></p>
<p class="MsoNormal">-----------------------------------------------------------<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I loaded the chromosomes.gff3 file with the following command:<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">bp_seqfeature_load.pl -d dbname=gbtest -a DBI::Pg -u xxx -p xxx -c -v chromosomes.gff3<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">And for the ideogram.gff3 and study_2.gff3 files, I use the commad:<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">bp_seqfeature_load.pl -d dbname=gbtest -a DBI::Pg -u xxx -p xxx –v <filename.gff3><o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I have tried to correct this error by defining the regions using the ##sequence-region pragma, however that results in a duplication of the chromosome region in my database. Is there a way to allow loading of multiple gff3 files, whose
parent IDs are already loaded into the database?<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">(P.S. program versions, example files are located past the signature)<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thanks<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span style="font-size:13.5pt;font-family:"Microsoft Sans Serif","sans-serif"">Nigel Wilson</span>
<br>
<span style="font-size:10.0pt;font-family:"Microsoft Sans Serif","sans-serif"">_________________________________________________</span>
<br>
<span style="font-size:10.0pt;font-family:"Microsoft Sans Serif","sans-serif"">Research Student</span>
<br>
<span style="font-size:10.0pt;font-family:"Microsoft Sans Serif","sans-serif"">The Centre for Applied Genomics</span><o:p></o:p></p>
<p class="MsoNormal">The Hospital for Sick Children, MaRS Building - East Tower<br>
<span style="font-size:10.0pt">­­­­­­­­­­­</span><span style="font-size:10.0pt;font-family:Wingdings">(</span><span style="font-size:
10.0pt">: 416.813.7032</span><br>
<b><span style="font-size:10.0pt;font-family:Wingdings">*</span></b><span style="font-size:10.0pt">: 101 College St., Rm 14-701, Toronto, Ontario M5G 1L7</span><o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Info<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">BioPerl Version -> latest bioperl-live<o:p></o:p></p>
<div style="mso-element:para-border-div;border:none;border-bottom:solid windowtext 1.0pt;
padding:0cm 0cm 1.0pt 0cm">
<p class="MsoNormal" style="border:none;padding:0cm">Gbrowse version: 2.10<o:p></o:p></p>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">File Examples:<o:p></o:p></p>
<p class="MsoNormal">Chromosomes.gff3<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">##gff-version 3<o:p></o:p></p>
<p class="MsoNormal">##Index-subfeatures 1<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">chr1 hg18 chromosome 1 247249719 . . . ID=chr1;Name=Chr1<o:p></o:p></p>
<p class="MsoNormal">chr10 hg18 chromosome 1 135374737 . . . ID=chr10;Name=Chr10<o:p></o:p></p>
<p class="MsoNormal">chr11 hg18 chromosome 1 134452384 . . . ID=chr11;Name=Chr11<o:p></o:p></p>
<div style="mso-element:para-border-div;border:none;border-bottom:solid windowtext 1.0pt;
padding:0cm 0cm 1.0pt 0cm">
<p class="MsoNormal" style="border:none;padding:0cm">chr12 hg18 chromosome 1 132349534 . . . ID=chr12;Name=Chr12<o:p></o:p></p>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">ideogram.gff3<o:p></o:p></p>
<p class="MsoNormal">##gff-version 3<o:p></o:p></p>
<p class="MsoNormal">##Index-subfeatures 1<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">chr1 UCSC cytoband 1 2300000 . . . Parent=chr1;Name=Cytoband:1p36.33;Alias=p36.33;stain=gneg;<o:p></o:p></p>
<p class="MsoNormal">chr1 UCSC cytoband 2300001 5300000 . . . Parent=chr1;Name=Cytoband:1p36.32;Alias=p36.32;stain=gpos25;<o:p></o:p></p>
<p class="MsoNormal">chr1 UCSC cytoband 5300001 7100000 . . . Parent=chr1;Name=Cytoband:1p36.31;Alias=p36.31;stain=gneg;<o:p></o:p></p>
<p class="MsoNormal">chr1 UCSC cytoband 7100001 9200000 . . . Parent=chr1;Name=Cytoband:1p36.23;Alias=p36.23;stain=gpos25;<o:p></o:p></p>
<div style="mso-element:para-border-div;border:none;border-bottom:solid windowtext 1.0pt;
padding:0cm 0cm 1.0pt 0cm">
<p class="MsoNormal" style="border:none;padding:0cm">chr1 UCSC cytoband 9200001 12600000 . . . Parent=chr1;Name=Cytoband:1p36.22;Alias=p36.22;stain=gneg;<o:p></o:p></p>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">study_2.gff3<o:p></o:p></p>
<p class="MsoNormal">##gff-version 3<o:p></o:p></p>
<p class="MsoNormal">##Index-subfeatures 1<o:p></o:p></p>
<p class="MsoNormal">chrX DGV2 sample_level_variant 136348080 136348238 . + . ID=abc_41;Parent=chrX;Name=abc_41;variant_type=CNV;gender=M;study=test 2009;<o:p></o:p></p>
<p class="MsoNormal">chr7 DGV2 sample_level_variant 7074153 7074960 . + . ID=abc_4025;Parent=chr7;Name=abc_4025;variant_type=CNV;gender=M;study=test 2009;<o:p></o:p></p>
<p class="MsoNormal">chr2 DGV2 sample_level_variant 41069334 41070418 . + . ID=abc_4023;Parent=chr2;Name=abc_4023;variant_type=CNV;gender=M;study=test 2009;<o:p></o:p></p>
<p class="MsoNormal">chr1 DGV2 sample_level_variant 71513720 71514441 . + . ID=abc_3923;Parent=chr1;Name=abc_3923;variant_type=CNV;gender=M;study=test 2009;<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
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