From c3e0bd6535b2e28b67874d8c45d8a326185cf5c3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jens=20Preu=C3=9Fner?= Date: Thu, 29 Oct 2015 09:21:05 +0100 Subject: [PATCH] Fixed command not found error due to trailing whitespace --- src/admire | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/admire b/src/admire index 0c5137e..3c76a57 100755 --- a/src/admire +++ b/src/admire @@ -466,7 +466,7 @@ print id,name,gid,type,$1,$2,$3,$6,$7,$8,$9,$10,higherin,qval,$14,$11,$12,$13;}' fi sort -t',' -k14,14n $EXCEL/$g-$r.csv | cut -d',' -f5,6,7 | sed -e 's/,/\t/g' | tail -n +2 | head -n $I > $VISUALIZATION/$g/$r-target.bed split -l 1 $VISUALIZATION/$g/$r-target.bed $VISUALIZATION/$g/$r-target- - targets = $(ls $VISUALIZATION/$g/$r-target-*) + targets=$(ls $VISUALIZATION/$g/$r-target-*) for f in $targets; do bedtools intersect -wa -a $DIR/../data/ilmn12.hg19.bed -b $f | awk 'BEGIN{FS="\t";OFS="\t";}{split($4,a,";");split(a[1],b,"=");print b[2],$2}' | sort > $f.probes cut -f1 $f.probes | grep -f - $WORKDIR/normalized/betaValues_fn.sorted.txt > $f.grep