Update to catalog2 creation following preservation method query

ding-lab · Mar 6, 2023 · 935e2d5 · 935e2d5
1 parent a8392f9
commit 935e2d5
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Showing 3 changed files with 9 additions and 3 deletions.
diff --git a/1_run_discovery.sh b/1_run_discovery.sh
@@ -6,7 +6,9 @@ mkdir -p logs
 LOGE="logs/1_run_discovery.err"
 LOGO="logs/1_run_discovery.out"
 
-CMD="bash src/run_discovery.sh $@ -J 10 -vvv -t $GDC_TOKEN $CASES  > $LOGO 2> $LOGE"
+NJOBS="5"
+
+CMD="bash src/run_discovery.sh $@ -J $NJOBS -vvv -t $GDC_TOKEN $CASES  > $LOGO 2> $LOGE"
 >&2 echo Running: $CMD
 >&2 echo Writing logs to $LOGO and $LOGE
 eval $CMD

diff --git a/src/make_catalog2.sh b/src/make_catalog2.sh
@@ -325,6 +325,7 @@ function get_SN {
 #    * sample submitter id
 #    * sample id
 #    * sample type
+#    * preservation method (NEW)
 #    * aliquot submitter id
 #    * aliquot id
 #    * analyte_type
@@ -333,9 +334,11 @@ function get_sample_type {
     ALIQUOT_NAME=$1
     ALIQUOTS_FN=$2
 
+#    >&2 echo DEBUG: get_sample_type ALIQUOT_NAME = $ALIQUOT_NAME  ALIQUOTS_FN = $ALIQUOTS_FN
+
 # Matching to ALIQUOT name with grep is inexact
 #    SAMPLE_TYPE=$(grep $ALIQUOT_NAME $ALIQUOTS_FN | cut -f 4 | sort -u)
-    SAMPLE_TYPE=$(awk -v AN=$ALIQUOT_NAME 'BEGIN{FS="\t";OFS="\t"}{if ($5 == AN ) print $4}' $ALIQUOTS_FN | sort -u)
+    SAMPLE_TYPE=$(awk -v AN=$ALIQUOT_NAME 'BEGIN{FS="\t";OFS="\t"}{if ($6 == AN ) print $4}' $ALIQUOTS_FN | sort -u)
     MATCH_COUNT=$(echo -n "$SAMPLE_TYPE" | grep -c '^')
     if [ $MATCH_COUNT == 0 ]; then
         >&2 echo ERROR: Sample type for aliquot $ALIQUOT_NAME not found in $ALIQUOTS_FN

diff --git a/src/queryGDC.sh b/src/queryGDC.sh
@@ -20,7 +20,8 @@
 
 # #########
 
-PYTHON="/usr/bin/python3"
+#PYTHON="/usr/bin/python3"
+PYTHON="/diskmnt/Projects/Users/mwyczalk/miniconda3/bin/python"
 JQ="jq"
 
 if ! command -v $JQ &> /dev/null