Shell script

viral.pipeline_public_final_1.sh

@@ -0,0 +1,78 @@
+#!/bin/bash
+
+# Alignment using Bowtie2
+functionBowtie2() {
+	echo "Start - Align using Bowtie2 local algin" >> $LOG
+	$BOWTIE2_SW"bowtie2" -x $BOWTIE2_REF --local -1 $I_FOLDER$ID"_1.fq" -2 $I_FOLDER$ID"_2.fq" --threads $N_THREAD --al $O_FOLDER$ID/$ID".bowtie2.align" --un $O_FOLDER$ID/$ID".Bowtie2.unaligned" -S $O_FOLDER$ID/$ID".bowtie2.sam" --sensitive > $O_FOLDER$ID/$ERR2 2> $O_FOLDER$ID/$ERR3
+	echo "End - Align using Bowtie2 local algin" >> $LOG
+}
+
+#Convert SAM file to BAM file
+functionConvertSamtoBam() {
+    echo "Start - convert sam to bam file using Samtools" >> $LOG
+	$SAMTOOLS"samtools" view -bS $O_FOLDER$ID/$ID".bowtie2.sam" > $O_FOLDER$ID/$ID".bowtie2.bam"
+    echo "End - convert sam to bam file using Samtools" >> $LOG
+}
+
+#Sort BAM coordinate wise
+functionSortBam() {
+    echo "Start - Samtools sort bam file" >> $LOG
+	$SAMTOOLS"samtools" sort $O_FOLDER$ID/$ID".bowtie2.bam" -o $O_FOLDER$ID/$ID".bowtie2.sorted.bam" -@ $N_THREAD
+    echo "End - Samtools sort bam file" >> $LOG
+} 
+
+#Index BAM file
+functionIndexBam() {
+    echo "Start - Samtools index bam file" >> $LOG
+	$SAMTOOLS"samtools" index $O_FOLDER$ID/$ID".bowtie2.sorted.bam"
+    echo "End - Samtools index bam file" >> $LOG
+}
+
+# Samtools idx -  genome level counts
+functionIdxStatsBam() {
+    echo "Start - Samtools Idx" >> $LOG
+	$SAMTOOLS"samtools" idxstats $O_FOLDER$ID/$ID".bowtie2.sorted.bam" > $O_FOLDER$ID/$ID".bowtie2.idxstats.txt"
+    echo "End - Samtools Idx" >> $LOG
+ }
+
+########################################
+# Values to set by the user
+N_THREAD=4
+I_FOLDER="/Users/ls483/Documents/SRA.GEO/input/unmapped_fastq/"
+O_FOLDER="/Users/ls483/Documents/SRA.GEO/output_bowtie2/"
+
+LOG=$O_FOLDER"/pipeline_log.txt"
+ERR2="system.err.bowtie2.txt"
+ERR3="log.bowtie2.txt"
+SAMTOOLS="/Users/ls483/Documents/software/samtools/bin/"
+BOWTIE2_SW="/Users/ls483/Documents/software/bowtie/bowtie2-2.2.9/"
+BOWTIE2_REF="/Users/ls483/Documents/SRA.GEO/viral.reference/virus.bowtie2.refB/virus.bowtie2.refB"
+
+for x in $(cat samplenames.txt)
+do
+    echo $x
+    ID=${x%*}
+
+    echo "-----------------------------" >> $LOG
+    echo $ID >> $LOG
+
+    START=$(date +%s) 
+
+    mkdir $O_FOLDER$ID
+
+    functionBowtie2
+
+    functionConvertSamtoBam
+
+    functionSortBam
+
+    functionIndexBam
+
+    functionIdxStatsBam
+
+    functionFlagstatBam
+
+	END=$(date +%s)
+	DIFF=$(( ($END - $START)/60 )) 
+	echo "It took $DIFF minutes" >> $LOG
+done