changeset 0:77a6b67de66d draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/FilterPeaks.sh	Tue Feb 09 08:43:06 2016 -0500
@@ -0,0 +1,65 @@
+#!/bin/bash
+
+nameBed=" "
+
+while getopts "f:c:t:v:m:r:o:w:b::n::q::l::" optionName; do
+case "$optionName" in
+
+f) inputfile="$OPTARG";;
+c) controlfile="$OPTARG";;
+t) minHeight="$OPTARG";;
+v) minRatio="$OPTARG";;
+m) minHeightControl="$OPTARG";;
+r) ROOT_DIR="$OPTARG";;
+o) output="$OPTARG";;
+w) outputControl="$OPTARG";;
+b) BEDFILE="$OPTARG";;
+n) nameBed="$OPTARG";;
+q) nameBedControl="$OPTARG";;
+l) BUILD="$OPTARG";;
+esac
+done
+
+local_path=/usr/bin/filterpeaks
+DATABASE_PATH=$ROOT_DIR/database/files
+mkdir -p $DATABASE_PATH/nebulaAnnotations
+mkdir -p $DATABASE_PATH/nebulaAnnotations/$BUILD
+nebulaAnnotationPath=$DATABASE_PATH/nebulaAnnotations
+nebulaGenomePath=$DATABASE_PATH/nebulaAnnotations/$BUILD
+
+#echo "$@" > /data/tmp/tmp.log
+echo "java -classpath local_path/ -Xmx6g FilterPeaks -f $inputfile -c $controlfile -t $minHeight -v $minRatio -o $output"
+java -classpath $local_path/ -Xmx6g FilterPeaks -f $inputfile -c $controlfile -t $minHeight -v $minRatio -o $output 
+java -classpath $local_path/ -Xmx6g FilterPeaks -c $inputfile -f $controlfile -t $minHeightControl -v $minRatio -o $outputControl
+
+if [ "$BEDFILE" == "yes" ]; then
+
+  ############### Create annotations files ################
+
+  FAIFILE='n'
+  LENFILE='n'
+  DICTFILE='n'
+  CHROFILE='n'
+  MAPFILE='n'
+
+  if [ ! -f $nebulaGenomePath/$BUILD.len ]; then
+      FAIFILE='y'
+      LENFILE='y'
+  fi
+  
+  chrom_info_file=$nebulaGenomePath/$BUILD.len
+  FILEPATH=$ROOT_DIR/tool-data
+  
+  bash /usr/bin/create_annotation_files.sh $FAIFILE $LENFILE $DICTFILE $CHROFILE $FILEPATH $BUILD $MAPFILE $nebulaGenomePath
+  
+  #################### END ANNOTATION FILES ###########################
+
+  perl $local_path/peak2bed.pl -f $output -t 0 -o $output.tmp -g $chrom_info_file -n $nameBed
+  perl $local_path/peak2bed.pl -f $outputControl -t 0 -o $outputControl.tmp -g $chrom_info_file -n $nameBedControl 
+  cp $output.tmp $output
+  rm $output.tmp
+  cp $outputControl.tmp $outputControl
+  rm $outputControl.tmp
+fi
+
+