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Add qualitative gene_ex data to load script

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commit e655685a44d23393ad612d34d5cfef0010dea096 1 parent 6e2a1f8
Kim Rutherford authored

Showing 1 changed file with 10 additions and 0 deletions. Show diff stats Hide diff stats

  1. +10 0 etc/load-all.sh
10 etc/load-all.sh
@@ -93,6 +93,16 @@ gzip -d < $CURRENT_GOA_GAF | kgrep '\ttaxon:(4896|284812)\t' | ./script/pombase-
93 93 echo annotation count after GAF loading:
94 94 evidence_summary
95 95
  96 +
  97 +echo load quantitative gene expression data
  98 +
  99 +for file in /var/pomcur/sources/quantitative_gene_expression/*
  100 +do
  101 + echo loading: $i
  102 + ./script/pombase-import.pl load-chado.yaml quantitative --organism_taxonid=9606 $HOST $DB $USER $PASSWORD < $file 2>&1 | tee $LOG_DIR/$log_file.quantitative
  103 +done
  104 +
  105 +
96 106 echo load Compara orthologs
97 107
98 108 ./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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