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base fork: kimrutherford/pombase-chado
base: 5cdb76da8d
...
head fork: kimrutherford/pombase-chado
compare: e655685a44
  • 2 commits
  • 2 files changed
  • 0 commit comments
  • 1 contributor
Showing with 11 additions and 1 deletion.
  1. +10 −0 etc/load-all.sh
  2. +1 −1  lib/PomBase/Import/Qualitative.pm
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10 etc/load-all.sh
@@ -93,6 +93,16 @@ gzip -d < $CURRENT_GOA_GAF | kgrep '\ttaxon:(4896|284812)\t' | ./script/pombase-
echo annotation count after GAF loading:
evidence_summary
+
+echo load quantitative gene expression data
+
+for file in /var/pomcur/sources/quantitative_gene_expression/*
+do
+ echo loading: $i
+ ./script/pombase-import.pl load-chado.yaml quantitative --organism_taxonid=9606 $HOST $DB $USER $PASSWORD < $file 2>&1 | tee $LOG_DIR/$log_file.quantitative
+done
+
+
echo load Compara orthologs
./script/pombase-import.pl load-chado.yaml orthologs --publication=PMID:19029536 --organism_1_taxonid=4896 --organism_2_taxonid=9606 --swap-direction $HOST $DB $USER $PASSWORD < $SOURCES/pombe-embl/orthologs/compara_orths.tsv 2>&1 | tee $LOG_DIR/$log_file.compara_orths
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2  lib/PomBase/Import/Qualitative.pm
@@ -58,7 +58,7 @@ has organism => (is => 'rw', init_arg => undef);
method BUILD
{
- my $organism_taxonid = '';
+ my $organism_taxonid = undef;
my @opt_config = ('organism_taxonid=s' => \$organism_taxonid);
if (!GetOptionsFromArray($self->options(), @opt_config)) {

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