Update SEACR_1.3.sh

Added filter in lines 101-103 and 109-111 to remove bed graph entries with zero signal
FredHutch · Jan 9, 2020 · 9269e0a · 9269e0a
1 parent cdeceee
commit 9269e0a
Showing 1 changed file with 4 additions and 4 deletions.
diff --git a/SEACR_1.3.sh b/SEACR_1.3.sh
@@ -98,16 +98,16 @@ fi
 
 echo "Creating experimental AUC file: $(date)"
 
-awk 'BEGIN{s=1}; {if(s==1){s++}else if(s==2){chr=$1; start=$2; stop=$3; max=$4; coord=$1":"$2"-"$3; auc=$4*($3-$2); num=1; s++}else{if(chr==$1 && $2==stop){num++; stop=$3; auc=auc+($4*($3-$2)); if ($4 > max){max=$4; coord=$1":"$2"-"$3
-}else if($4 == max){split(coord,t,"-"); coord=t[1]"-"$3}}else{print chr"\t"start"\t"stop"\t"auc"\t"max"\t"coord"\t"num; chr=$1; start=$2; stop=$3; max=$4; coord=$1":"$2"-"$3; auc=$4*($3-$2); num=1}}}' $1 > $password.auc.bed
+awk 'BEGIN{s=1}; {if(s==1){s++}else if(s==2){if($4 > 0){chr=$1; start=$2; stop=$3; max=$4; coord=$1":"$2"-"$3; auc=$4*($3-$2); num=1; s++}}else{if($4 > 0){if(chr==$1 && $2==stop){num++; stop=$3; auc=auc+($4*($3-$2)); if ($4 > max){max=$4; coord=$1":"$2"-"$3
+}else if($4 == max){split(coord,t,"-"); coord=t[1]"-"$3}}else{print chr"\t"start"\t"stop"\t"auc"\t"max"\t"coord"\t"num; chr=$1; start=$2; stop=$3; max=$4; coord=$1":"$2"-"$3; auc=$4*($3-$2); num=1}}}}' $1 > $password.auc.bed
 cut -f 4,7 $password.auc.bed > $password.auc
 
 if [[ -f $2 ]]
 then
   echo "Creating control AUC file: $(date)"
 
-  awk 'BEGIN{s=1}; {if(s==1){s++}else if(s==2){chr=$1; start=$2; stop=$3; max=$4; coord=$1":"$2"-"$3; auc=$4*($3-$2); num=1; s++}else{if(chr==$1 && $2==stop){num++; stop=$3; auc=auc+($4*($3-$2)); if ($4 > max){max=$4; coord=$1":"$2"-"
-$3}else if($4 == max){split(coord,t,"-"); coord=t[1]"-"$3}}else{print chr"\t"start"\t"stop"\t"auc"\t"max"\t"coord"\t"num; chr=$1; start=$2; stop=$3; max=$4; coord=$1":"$2"-"$3; auc=$4*($3-$2); num=1}}}' $2 > $password2.auc.bed
+  awk 'BEGIN{s=1}; {if(s==1){s++}else if(s==2){if($4 > 0){chr=$1; start=$2; stop=$3; max=$4; coord=$1":"$2"-"$3; auc=$4*($3-$2); num=1; s++}}else{if($4 > 0){if(chr==$1 && $2==stop){num++; stop=$3; auc=auc+($4*($3-$2)); if ($4 > max){max=$4; coord=$1":"$2"-"
+$3}else if($4 == max){split(coord,t,"-"); coord=t[1]"-"$3}}else{print chr"\t"start"\t"stop"\t"auc"\t"max"\t"coord"\t"num; chr=$1; start=$2; stop=$3; max=$4; coord=$1":"$2"-"$3; auc=$4*($3-$2); num=1}}}}' $2 > $password2.auc.bed
   cut -f 4,7 $password2.auc.bed > $password2.auc
 fi