Add normalized signal and gene expression.

gene-counts.sh

+#!/bin/bash
+# gene-counts.sh
+
+script_name="gene-counts.sh"
+script_ver="1.0.0"
+
+#Help function
+usage() {
+  echo "-h Help documentation for $script_name"
+  echo "-a  --Path to bam file"
+  echo "-b  --Path to bam file2"
+  echo "-g  --Path to the annotation file"
+  echo "-o  --Path to output directory"
+  echo "-e  --The experiment names."
+  echo "-v  --Version of script"
+  echo "Example: $script_name -a 'foo_1.bam' -b 'foo_2.bam' -g '/path/to/gtf/gencode.v19.annotation.gtf' [-o '/path/to/output/dir/']"
+  exit 1
+}
+
+# Version function
+version(){
+    echo "$script_name $script_ver"
+    exit 1
+}
+
+main(){
+
+
+    # Load required modules
+    module load RSEM/1.2.31
+    module load python/2.7.x-anaconda
+    module load picard/1.127
+
+    # Parsing options
+    OPTIND=1 # Reset OPTIND
+    while getopts :a:b:s:g:e:o:vh opt
+        do
+            case $opt in
+                a) aln_file_2=$OPTARG;;
+		b) aln_file_1=$OPTARG;;
+                g) transcriptome=$OPTARG;;
+		e) exp=$OPTARG;;
+                o) out=$OPTARG;;
+                v) version;;
+                h) usage;;
+            esac
+        done
+
+    shift $(($OPTIND -1))
+
+    # Check for mandatory options
+    if [[ -z $aln_file_1 ]] || [[ -z $aln_file_2 ]] || [[ -z $transcriptome ]] || [[ -z $exp ]]; then
+        usage
+    fi
+
+    # Define the output directory, if none defined make the location relative to first file
+    if [ -z $out ]; then
+        one_parent=$(dirname "${aln_file_1}")
+        out_dir=$(dirname "${one_parent}")\/$script_name-$script_ver/
+    else
+        out_dir=$out\/$script_name-$script_ver
+    fi
+
+    if [ ! -d $out_dir ]; then
+        mkdir $out_dir
+    fi
+
+
+    # If filtered alignment file doesn't exist
+    if [ ! -e $out_dir/$exp.counts ]; then
+
+
+	java -Xmx2g -jar $PICARD/picard.jar MergeSamFiles OUTPUT=$out_dir/$exp.bam INPUT=$aln_file_1 INPUT=$aln_file_2
+
+	rsem-calculate-expression -p 32 --bam --estimate-rspd --calc-ci --seed 12345 --no-bam-output --ci-memory 30000  $out_dir/$exp.bam $transcriptome $out_dir/$output_fp
+
+	rm $out_dir/$exp.bam
+
+        # Get input and output files and then print out metadata.json file
+        input_files=("$aln_file_1", "$aln_file_2", "$transcriptome")
+        printf -v input "\"%s\"," "${input_files[@]}"
+        input=${input%,}
+        output_file=($out_dir/$output_fp*)
+        printf -v output "\"%s\"," "${output_file[@]}"
+        output=${output%,}
+        printf '{"script name":"%s","script version":"%s", "input files": [%s], "output files": [%s]}' "$script_name" "$script_ver" "$input" "$output"  | python -m json.tool > $out_dir/$output_fp.metadata.json
+
+    else
+        echo "* Counts have already been called for $raw_fn"
+    fi
+}
+
+main "$@"

make-normal-signal.sh

+#!/bin/bash
+# make-normal-signal.sh
+
+script_name="make-normal-signal.sh"
+script_ver="1.0.0"
+
+#Help function
+usage() {
+  echo "-h Help documentation for $script_name"\\n
+  echo "-f --File path to Replicate 1 alignment."
+  echo "-s --File path to Replicate 2 alignment."
+  echo "-r  --UCSC Reference genome (e.g. hg19, mm10)"
+  echo "-e  --The experiment names."
+  echo "-o  --The ouput directory."
+  echo "Example: $script_name -f 'foo1.bam' -s 'foo2.bam man2.bam' -r 'hg19' -e 'foo man' -o output"
+  exit 1
+}
+
+# Version function
+version(){
+    echo "$script_name $script_ver"
+    exit 1
+}
+
+main(){
+
+    # Load required modules
+    module load python/2.7.x-anaconda
+    module load star/2.4.2a
+    module load picard/1.127
+    module load UCSC_userApps/v317
+
+    # Parsing options
+    OPTIND=1 # Reset OPTIND
+    while getopts :f:s:r:e:o:hv opt
+        do
+            case $opt in
+                f) aln1=$OPTARG;;
+                s) aln2=$OPTARG;;
+                r) ucsc_reference=$OPTARG;;
+                e) exp=$OPTARG;;
+                o) out=$OPTARG;;
+                h) usage;;
+                v) version;;
+            esac
+        done
+
+    shift $(($OPTIND -1))
+
+    # Check for mandatory options
+    if [[ -z $aln1 ]] || [[ -z $aln2 ]] || [[ -z $ucsc_reference ]] || [[ -z $exp ]] || [[ -z $out ]]; then
+        usage
+    fi
+
+    # Define the out directory
+    out_dir=$out\/$script_name-$script_ver
+
+    # Make sure directories exist
+    if [ ! -e $out ]; then
+        mkdir $out
+    fi
+
+    # Run make-normal-signal.R if directory doesn't exist
+    if [ ! -d $out_dir ]; then
+        mkdir $out_dir
+        # Fetch chrom sizes
+        echo "* Downloading chrom.sizes..."
+        fetchChromSizes $ucsc_reference > $out_dir/chrom.sizes
+
+        java -Xmx2g -jar $PICARD/picard.jar MergeSamFiles OUTPUT=$out_dir/$exp.bam INPUT=$aln1 INPUT=$aln2
+        cd $out_dir
+        STAR --runMode inputAlignmentsFromBAM --inputBAMfile $exp.bam --outWigType bedGraph --outWigStrand Stranded --outFileNamePrefix $exp --outWigReferencesPrefix chr
+        bedSort $out_dir/$exp\Signal.UniqueMultiple.str1.out.bg $out_dir/$exp\Signal.UniqueMultiple.str1.out.sorted.bg
+        bedSort $out_dir/$exp\Signal.UniqueMultiple.str2.out.bg $out_dir/$exp\Signal.UniqueMultiple.str2.out.sorted.bg
+        bedGraphToBigWig $out_dir/$exp\Signal.UniqueMultiple.str1.out.sorted.bg $out_dir/chrom.sizes $out_dir/$exp.negative.bw
+        bedGraphToBigWig $out_dir/$exp\Signal.UniqueMultiple.str2.out.sorted.bg $out_dir/chrom.sizes $out_dir/$exp.positive.bw
+        rm $out_dir/$exp*.bg
+        rm $out_dir/$exp.bam
+
+        # Get input and output files and then print out metadata.json file
+        input_files=("${array_aln1[@]}" "${array_aln2[@]}")
+        printf -v input "\"%s\"," "${input_files[@]}"
+        input=${input%,}
+        output_file=($out_dir\/*)
+        printf -v output "\"%s\"," "${output_file[@]}"
+        output=${output%,}
+        printf '{"script name":"%s","script version":"%s", "input files": [%s], "output files": [%s]}' "$script_name" "$script_ver" "$input" "$output"  | python -m json.tool > $out_dir/metadata.json
+    else
+        echo "* Normalized Signal has been made. "
+    fi
+}
+
+main "$@"