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First stab at organizing fs

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This commit is contained in:
Bryan Roessler
2024-07-28 05:54:41 -04:00
parent 8de5005055
commit e734dcd93a
2 changed files with 11 additions and 17 deletions
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1
workflow/apps/r/joinInteractExps.R
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@@ -30,7 +30,6 @@ if (length(args) > 3) {
} }
studies <- args[3:length(args)] studies <- args[3:length(args)]
inputFiles <- c() inputFiles <- c()
for (study in 1:length(studies)) { for (study in 1:length(studies)) {
zsFile <- file.path(study, 'zscores', 'zscores_interaction.csv') zsFile <- file.path(study, 'zscores', 'zscores_interaction.csv')

27
workflow/qhtcp-workflow
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@@ -807,8 +807,8 @@ qhtcp() {
r_interactions \ r_interactions \
"$STUDY_DIR" \ "$STUDY_DIR" \
"$STUDY_INFO_FILE" \ "$STUDY_INFO_FILE" \
"$STUDY_DIR/ZScores/" \ "$STUDY_DIR/zscores/" \
"$CODE_DIR/SGD_features.tab" \ "$APPS_DIR/r/SGD_features.tab" \
5 5
done done
@@ -904,15 +904,15 @@ module gta
gta() { gta() {
debug "Running: ${FUNCNAME[0]}" debug "Running: ${FUNCNAME[0]}"
GTA_OUT_DIR="$QHTCP_PROJECT_DIR/GTAresults" GTA_OUT_DIR="$QHTCP_PROJECT_DIR/gta"
all_sgd_terms_csv="$CODE_DIR/All_SGD_GOTerms_for_QHTCPtk.csv" all_sgd_terms_csv="$APPS_DIR/r/All_SGD_GOTerms_for_QHTCPtk.csv"
sgd_terms_tfile="$CODE_DIR/go_terms.tab" sgd_terms_tfile="$APPS_DIR/r/go_terms.tab"
sgd_features_file="$CODE_DIR/gene_association.sgd" sgd_features_file="$APPS_DIR/r/gene_association.sgd"
gene_ontology_file="$CODE_DIR/gene_ontology_edit.obo" gene_ontology_file="$APPS_DIR/r/gene_ontology_edit.obo"
zscores_file="ZScores/ZScores_Interaction.csv" zscores_file="zscores/zscores_interaction.csv"
# Sets STUDIES_NUM and NUM_STUDIES # Sets STUDIES_NUM and NUM_STUDIES
get_studies get_studies "$STUDY_INFO_FILE"
[[ -d $GTA_OUT_DIR ]] || mkdir "$GTA_OUT_DIR" [[ -d $GTA_OUT_DIR ]] || mkdir "$GTA_OUT_DIR"
@@ -958,10 +958,6 @@ gta() {
# All studies # All studies
# If you have an unknown # of studies it must be passed last and any preceding arguments # If you have an unknown # of studies it must be passed last and any preceding arguments
# are required # are required
#
#
#
#
r_gta_heatmaps \ r_gta_heatmaps \
"$STUDY_INFO_FILE" \ "$STUDY_INFO_FILE" \
"$gene_ontology_file" \ "$gene_ontology_file" \
@@ -971,7 +967,6 @@ gta() {
"$QHTCP_PROJECT_DIR" \ "$QHTCP_PROJECT_DIR" \
"$QHTCP_PROJECT_DIR/TermSpecificHeatmaps" \ "$QHTCP_PROJECT_DIR/TermSpecificHeatmaps" \
"${STUDIES_NUMS[@]}" "${STUDIES_NUMS[@]}"
} }
@@ -1014,7 +1009,7 @@ r_gta() {
EOF EOF
script="$CODE_DIR/GTAtemplate.R" script="$APPS_DIR/r/GTAtemplate.R"
[[ -d $5 ]] || mkdir -p "$5" [[ -d $5 ]] || mkdir -p "$5"
@@ -1051,7 +1046,7 @@ r_gta_pairwiselk() {
EOF EOF
script="$CODE_DIR/PairwiseLK.R" script="$APPS_DIR/r/PairwiseLK.R"
[[ -d $4 ]] || mkdir -p "$4" [[ -d $4 ]] || mkdir -p "$4"