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From: Scott C. <sco...@us...> - 2009-02-11 16:58:01
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Update of /cvsroot/gmod/schema/chado/load/bin In directory ddv4jf1.ch3.sourceforge.com:/tmp/cvs-serv9381 Modified Files: bulk_load_gff3.PLS Log Message: fix for change in bioperl api for Bio::Annotation::Target objects Index: bulk_load_gff3.PLS =================================================================== RCS file: /cvsroot/gmod/schema/chado/load/bin/bulk_load_gff3.PLS,v retrieving revision 1.87 retrieving revision 1.88 diff -C2 -d -r1.87 -r1.88 *** bulk_load_gff3.PLS 8 Dec 2008 16:44:50 -0000 1.87 --- bulk_load_gff3.PLS 11 Feb 2009 16:57:49 -0000 1.88 *************** *** 859,865 **** # if (!$analysis_err_str && !$ANALYSIS && ( ! ((scalar($feature->annotation->get_Annotations('Target'))>0) and ! ($feature->annotation->get_Annotations('Target'))[0]->value) or ! (defined($feature->score) and $feature->score ne '.') or $featuretype =~ /match/ ) ) { --- 859,872 ---- # if (!$analysis_err_str && !$ANALYSIS && ( ! ((scalar($feature->annotation->get_Annotations('Target'))>0) ! and ! ((($feature->annotation->get_Annotations('Target'))[0]->can('value') ! && ($feature->annotation->get_Annotations('Target'))[0]->value) ! or ! (($feature->annotation->get_Annotations('Target'))[0]->can('display_text') ! && ($feature->annotation->get_Annotations('Target'))[0]->display_text))) ! or ! (defined($feature->score) and $feature->score ne '.') ! or $featuretype =~ /match/ ) ) { *************** *** 881,885 **** && $featuretype =~ /match/ && !defined($feature->annotation->get_Annotations('Target'))) { ! $chado->cache('feature',($feature->annotation->get_Annotations('ID'))[0]->value,$nextfeature); } --- 888,902 ---- && $featuretype =~ /match/ && !defined($feature->annotation->get_Annotations('Target'))) { ! if (($feature->annotation->get_Annotations('ID'))[0]->can('value')) { ! $chado->cache('feature', ! ($feature->annotation->get_Annotations('ID'))[0]->value, ! $nextfeature); ! } ! elsif (($feature->annotation->get_Annotations('ID'))[0]->can('display_text')) { ! $chado->cache('feature', ! ($feature->annotation->get_Annotations('ID'))[0]->display_text, ! $nextfeature); ! } ! } |