Commit 0ef244af authored by Leon-Charles Tranchevent's avatar Leon-Charles Tranchevent
Browse files

Correcting typo in GEO bash variable name.

parent aaf736be
......@@ -15,7 +15,7 @@ echo "== Submit dir. : ${SLURM_SUBMIT_DIR}"
echo ""
# Defining global parameters.
GEO_PLAFORM_FOLDER=/home/users/ltranchevent/Data/GeneDER/Original/Platforms/
GEO_PLATFORM_FOLDER=/home/users/ltranchevent/Data/GeneDER/Original/Platforms/
OUTPUT_FOLDER=/home/users/ltranchevent/Data/GeneDER/Analysis/03/
CODE_FOLDER=/home/users/ltranchevent/Projects/GeneDER/Analysis/03-Predict_missing/
......@@ -45,12 +45,12 @@ do
if [ "${platformGEOName}" != "NA" ]
then
# We use the GEO data
cut -f 1 ${GEO_PLAFORM_FOLDER}${platformGEOName}_chromX.tsv > ${OUTPUT_FOLDER}${platformName}_chromX.tsv
cut -f 1 ${GEO_PLAFORM_FOLDER}${platformGEOName}_chromY.tsv > ${OUTPUT_FOLDER}${platformName}_chromY.tsv
cut -f 1 ${GEO_PLATFORM_FOLDER}${platformGEOName}_chromX.tsv > ${OUTPUT_FOLDER}${platformName}_chromX.tsv
cut -f 1 ${GEO_PLATFORM_FOLDER}${platformGEOName}_chromY.tsv > ${OUTPUT_FOLDER}${platformName}_chromY.tsv
else
# We use manually curated data.
cut -f 1 ${GEO_PLAFORM_FOLDER}${platformName}_chromX.tsv > ${OUTPUT_FOLDER}${platformName}_chromX.tsv
cut -f 1 ${GEO_PLAFORM_FOLDER}${platformName}_chromY.tsv > ${OUTPUT_FOLDER}${platformName}_chromY.tsv
cut -f 1 ${GEO_PLATFORM_FOLDER}${platformName}_chromX.tsv > ${OUTPUT_FOLDER}${platformName}_chromX.tsv
cut -f 1 ${GEO_PLATFORM_FOLDER}${platformName}_chromY.tsv > ${OUTPUT_FOLDER}${platformName}_chromY.tsv
fi
fi
done
......
......@@ -15,7 +15,7 @@ echo "== Submit dir. : ${SLURM_SUBMIT_DIR}"
echo ""
# Defining global parameters.
GEO_PLAFORM_FOLDER=/home/users/ltranchevent/Data/GeneDER/Original/Platforms/
GEO_PLATFORM_FOLDER=/home/users/ltranchevent/Data/GeneDER/Original/Platforms/
OUTPUT_FOLDER=/home/users/ltranchevent/Data/GeneDER/Analysis/04/
CODE_FOLDER=/home/users/ltranchevent/Projects/GeneDER/Analysis/04-Prepare_datasets/
......@@ -37,7 +37,7 @@ do
if [ "${platformBiomartName}" != "NA" ]
then
# Get the official gene names.
wget -O ${OUTPUT_FOLDER}${platformName}_genenames_raw.tsv 'http://www.ensembl.org/biomart/martservice?query=<?xml version="1.0" encoding="UTF-8"?><!DOCTYPE Query><Query virtualSchemaName = "default" formatter = "TSV" header = "0" uniqueRows = "1" count = "" datasetConfigVersion = "0.6"><Dataset name = "hsapiens_gene_ensembl" interface = "default"><Attribute name = "'${platformBiomartName}'"/><Attribute name = "external_gene_name"/></Dataset></Query>'
wget -O ${OUTPUT_FOLDER}${platformName}_genenames_raw.tsv 'http://www.ensembl.org/biomart/martservice?query=<?xml version="1.0" encoding="UTF-8"?><!DOCTYPE Query><Query virtualSchemaName = "default" formatter = "TSV" header = "0" uniqueRows = "1" count = "" datasetConfigVersion = "0.6"><Dataset name = "hsapiens_gene_ensembl" interface = "default"><Filter name = "biotype" value = "protein_coding"/><Attribute name = "'${platformBiomartName}'"/><Attribute name = "external_gene_name"/></Dataset></Query>'
awk 'BEGIN{FS=OFS="\t"}{if ($1 != "") {print $0}}' ${OUTPUT_FOLDER}${platformName}_genenames_raw.tsv | awk '{if (t[$1]) {t[$1]=t[$1]"|"$2} else {t[$1]=$2}} END{for (i in t) {if (i != "") {print i"\t"t[i]}}}' | sort -u > ${OUTPUT_FOLDER}${platformName}_genenames.tsv
rm ${OUTPUT_FOLDER}${platformName}_genenames_raw.tsv
sleep 2s
......@@ -45,10 +45,10 @@ do
if [ "${platformGEOName}" != "NA" ]
then
# We use the GEO data
cut -f -2 ${GEO_PLAFORM_FOLDER}${platformGEOName}_gene_official.tsv | grep -v OFFICIAL | sort -u > ${OUTPUT_FOLDER}${platformName}_genenames.tsv
cut -f -2 ${GEO_PLATFORM_FOLDER}${platformGEOName}_gene_official.tsv | grep -v OFFICIAL | sort -u > ${OUTPUT_FOLDER}${platformName}_genenames.tsv
else
# We use manually curated data.
cut -f -2 ${GEO_PLAFORM_FOLDER}${platformName}_gene_official.tsv | grep -v OFFICIAL | sort -u > ${OUTPUT_FOLDER}${platformName}_genenames.tsv
cut -f -2 ${GEO_PLATFORM_FOLDER}${platformName}_gene_official.tsv | grep -v OFFICIAL | sort -u > ${OUTPUT_FOLDER}${platformName}_genenames.tsv
fi
fi
done
......
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