# HG changeset patch
# User ldelisle
# Date 1666168226 0
# Node ID 07695b197e6c54a2ec5e82cb491d81e5e94d5e6d

Uploaded

diff -r 000000000000 -r 07695b197e6c revertR2orientationInBam/.shed.yml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/revertR2orientationInBam/.shed.yml	Wed Oct 19 08:30:26 2022 +0000
@@ -0,0 +1,6 @@
+categories:
+   - SAM
+description: Revert the mapped orientation of R2 mates in a bam.
+name: revertr2orientationinbam
+owner: lldelisle
+long_description: This tool is very useful when you have paired-end stranded RNA-seq. Using this tool prior to a bedtools genome coverage allow to have strand specific coverage using both mates. It uses samtools to convert input to sam format and then awk to modify the flag "reverse strand" for the second mate of pairs.
diff -r 000000000000 -r 07695b197e6c revertR2orientationInBam/revertR2orientationInBam.sh
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/revertR2orientationInBam/revertR2orientationInBam.sh	Wed Oct 19 08:30:26 2022 +0000
@@ -0,0 +1,28 @@
+#!/bin/bash
+
+inputBam=$1
+outputBam=$2
+
+samtools view -h "$inputBam" | awk -v OFS="\t" '{
+    # Process only non header lines
+    if(!($1~/^@/)){
+        # SAM flag is field 2
+        n=$2
+        # Change only the second in pair flag is 128
+        d=128
+        q=(n-n%d)/d+(n<0)
+        if(q%2==1){
+            # Evaluate the strand reverse strand flag is 16
+            d=16
+            q=(n-n%d)/d+(n<0)
+            if(q%2==1){
+                # It is reverse it is now forward
+                $2-=16
+            }else{
+                # It is forward it is now reverse
+                $2+=16
+            }
+        }
+    }
+    print
+}' | samtools view -b - > "$outputBam"
\ No newline at end of file
diff -r 000000000000 -r 07695b197e6c revertR2orientationInBam/revertR2orientationInBam.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/revertR2orientationInBam/revertR2orientationInBam.xml	Wed Oct 19 08:30:26 2022 +0000
@@ -0,0 +1,40 @@
+<tool id="revertR2orientationInBam" name="revertR2orientationInBam" version="0.0.1" profile="16.04">
+  <description> Revert the mapped orientation of R2 mates in a bam.</description>
+  <requirements>
+    <requirement type="package" version="1.9">samtools</requirement>
+  </requirements>
+  <stdio>
+    <!-- Anything other than zero is an error -->
+    <exit_code range="1:" />
+    <exit_code range=":-1" />
+    <!-- In case the return code has not been set propery check stderr too -->
+    <regex match="Error:" />
+    <regex match="Exception:" />
+  </stdio>
+  <command>
+<![CDATA[
+        bash $__tool_directory__/revertR2orientationInBam.sh $input $output
+]]>
+  </command>
+  <inputs>
+    <!-- note unsorted bam includes all derived bam types (inlcuding bam which is sorted) -->
+    <param name="input" type="data" format="sam,bam" label="Select a sam or bam file."/>
+  </inputs>
+  <outputs>
+    <data format="bam" name="output" label="$input.name with R2 orientation reversed"/>
+  </outputs>
+
+  <tests>
+    <test>
+      <param name="input" value="input.sam"/>
+      <output name="output" file="output.bam" ftype="bam"/>
+    </test>
+  </tests>  
+  <help>
+<![CDATA[
+    This tool is very useful when you have paired-end stranded RNA-seq.
+    Using this tool prior to a bedtools genome coverage allow to have strand specific coverage using both mates.
+    It uses samtools to convert input to sam format and then awk to modify the flag "reverse strand" for the second mate of pairs.
+]]>
+  </help>
+</tool>
diff -r 000000000000 -r 07695b197e6c revertR2orientationInBam/test-data/input.sam
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/revertR2orientationInBam/test-data/input.sam	Wed Oct 19 08:30:26 2022 +0000
@@ -0,0 +1,7 @@
+@HD	VN:1.4	SO:coordinate
+@SQ	SN:chr1	LN:195471971
+1	163	chr1	3151308	255	43M	=	3151560	295	GTCCCAAAAAGCAGAGAGAAATATCTCTCTGGGCCTTATAGCA	AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE	NH:i:1 HI:i:1 AS:i:82 nM:i:1
+1	83	chr1	3151560	255	43M	=	3151308	-295	CTGCTGGAAAAACTGTTCGTTTTAGGAAATAAGGGCGAGTGCG	EEEEEEAEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEAAAAA	NH:i:1 HI:i:1 AS:i:82 nM:i:1
+2	137	chr1	3155261	255	9S20M	*	0	0	TGTGGGTTTTACACACGGGAGGAATCGGG	AAAAA/EEE/EE6EAEE6EAE6/EEEAEE	NH:i:1 HI:i:1 AS:i:19 nM:i:0
+3	99	chr1	3195817	255	43M	=	3195911	137	ATCTTACTCTGTTTCACAGATAGGTGCTGAGGTTAAATTTTGC	AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE	NH:i:1 HI:i:1 AS:i:84 nM:i:0
+3	147	chr1	3195911	255	43M	=	3195817	-137	GGTGTAGGTTCTTAGACGCAAGAAATCTCAGGTAGAGTTTGGC	EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA	NH:i:1 HI:i:1 AS:i:84 nM:i:0
diff -r 000000000000 -r 07695b197e6c revertR2orientationInBam/test-data/output.bam
Binary file revertR2orientationInBam/test-data/output.bam has changed