rule for calculating frip in replicate peaks

dunnart/Snakefile

@@ -636,6 +636,20 @@ rule overlap_peaks_H3K27ac:
     shell:
         "python2.7 scripts/overlap_peaks.py {input.peak1} {input.peak2} {input.pooled} {output}"
 
+## Fraction of reads in peaks
+rule overlap_frip:
+    input:
+        H3K4me3bam = "results/bowtie2/H3K4me3_pooled_PPq30.sorted.dedup.bam",
+        H3K27acbam = "results/bowtie2/H3K27ac_pooled_PPq30.sorted.dedup.bam",
+        H3K4me3bed = "results/macs2/H3K4me3_overlap.narrowPeak",
+        H3K27acbed = "results/macs2/H3K27ac_overlap.narrowPeak"
+    output:
+        H3K4me3frip = "results/qc/H3K4me3_overlap.frip",
+        H3K27acfrip = "results/qc/H3K27ac_overlap.frip"
+    run:
+        shell("python2.7 scripts/encode_frip.py {input.H3K4me3bam} {input.H3K4me3bed} > {output.H3K4me3frip}")
+        shell("python2.7 scripts/encode_frip.py {input.H3K27acbam} {input.H3K27acbed} > {output.H3K27acfrip}")
+
 # ===============================================================================================
 #  10. Combine all QC into multiqc output
 # ===============================================================================================