Commit 1e1d7166 authored by David Hoksza's avatar David Hoksza
Browse files

extension of genes integrated

parent e8dc2ac4
......@@ -54,11 +54,11 @@ genes_out_path=${genes_variants_out_path/02-genes_variants/03-genes}
echo ${genes_line#*:} | tr ',' '\n' > ${genes_out_path}
echo "Genes stored in ${genes_out_path}"
#echo "Extending genes list"
#text_mining_out_path=${genes_out_path/03-genes/03-text-mining}
#echo Rscript --vanilla ${EXTEND_DIR}/get_extended_network.R ${genes_out_path} ${EXTEND_CONFIG}
#cp ${EXTEND_DIR}/output.txt ${text_mining_out_path}
#echo "Genes list extended"
echo "Extending genes list"
text_mining_out_path=${genes_out_path/03-genes/03-text-mining}
echo Rscript --vanilla ${EXTEND_DIR}/get_extended_network.R ${genes_out_path} ${EXTEND_CONFIG}
cp ${EXTEND_DIR}/output.txt ${text_mining_out_path}
echo "Genes list extended"
minerva_genes_out_path=${RES_DIR}/04-minerva-genes.txt
$PYTHON_BIN $ASSOCIATIONS_DIR/minerva_genes.py -f ${genes_out_path} > ${minerva_genes_out_path}
......@@ -100,9 +100,9 @@ fi
echo "Map generator built"
echo "Assembling the map from pathways ..."
map_out_path=${RES_DIR}/06-minerva_map.xml
#java -Xmx4g -jar ${MAP_GENERATOR_DIR}/biohackathon/target/biohackathon-1.0-jar-with-dependencies.jar --enrichr-file ${enriched_paths_out_path} --minerva-file ${enriched_maps_out_path} --text-mining-file ${text_mining_out_path} --output-file ${map_out_path}
java -Xmx4g -jar ${MAP_GENERATOR_DIR}/biohackathon/target/biohackathon-1.0-jar-with-dependencies.jar --enrichr-file ${enriched_paths_out_path} --minerva-file ${enriched_maps_out_path} --output-file ${map_out_path}
echo "Pathways assembled into ${map_out_path}"
java -Xmx4g -jar ${MAP_GENERATOR_DIR}/biohackathon/target/biohackathon-1.0-jar-with-dependencies.jar --enrichr-file ${enriched_paths_out_path} --minerva-file ${enriched_maps_out_path} --text-mining-file ${text_mining_out_path} --output-file ${map_out_path}
#java -Xmx4g -jar ${MAP_GENERATOR_DIR}/biohackathon/target/biohackathon-1.0-jar-with-dependencies.jar --enrichr-file ${enriched_paths_out_path} --minerva-file ${enriched_maps_out_path} --output-file ${map_out_path}
echo "Pathwaygs assembled into ${map_out_path}"
echo "Combining map with overlays"
......
......@@ -84,6 +84,8 @@ if (dbsource == "stringdb") {
filters = 'ensembl_peptide_id',
values = protein_info$protein,
mart = ensembl)
biomartCacheClear()
protein_info_2ensp <- subset(protein_info_2ensp, ensembl_peptide_id != "")
protein_info_2ensp$ensembl_peptide_id <- paste0("9606.", protein_info_2ensp$ensembl_peptide_id)
......@@ -116,11 +118,12 @@ if (dbsource == "stringdb") {
colnames(result)[which(names(result) == "source_genesymbol")] <- "source_hgnc_symbol"
colnames(result)[which(names(result) == "target_genesymbol")] <- "target_hgnc_symbol"
gene_info_2entrez <- getBM(attributes=c('hgnc_symbol', 'entrezgene_id'),
filters = 'hgnc_symbol',
values = c(result$source_hgnc_symbol, result$target_hgnc_symbol),
mart = ensembl)
biomartCacheClear()
gene_info_2entrez <- subset(gene_info_2entrez, entrezgene_id != "")
result <- merge(result, gene_info_2entrez, by.x = "source_hgnc_symbol", by.y = "hgnc_symbol" )
......
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