commented out to fix bug later

mouse/Snakefile

@@ -554,50 +554,27 @@ rule frip:
 # Based on ENCODE `overlap_peaks.py` - recommended for histone marks.
 # Need to pool peaks first for each replicate
 
-rule pool_peaks:
-    input:
-        E10 = expand(["results/macs2/{case}_vs_{control}_E10.5_{mark}_macs2_peaks.narrowPeak"], zip, case=IPS, control=INPUTS, mark=MARK),
-        E11 = expand(["results/macs2/{case}_vs_{control}_E11.5_{mark}_macs2_peaks.narrowPeak"], zip, case=IPS, control=INPUTS, mark=MARK),
-        E12 = expand(["results/macs2/{case}_vs_{control}_E12.5_{mark}_macs2_peaks.narrowPeak"], zip, case=IPS, control=INPUTS, mark=MARK),
-        E13 = expand(["results/macs2/{case}_vs_{control}_E13.5_{mark}_macs2_peaks.narrowPeak"], zip, case=IPS, control=INPUTS, mark=MARK),
-        E14 = expand(["results/macs2/{case}_vs_{control}_E14.5_{mark}_macs2_peaks.narrowPeak"], zip, case=IPS, control=INPUTS, mark=MARK),
-        E15 = expand(["results/macs2/{case}_vs_{control}_E15.5_{mark}_macs2_peaks.narrowPeak"], zip, case=IPS, control=INPUTS, mark=MARK)
-    output:
-        E10 = expand("results/macs2/E10.5_{mark}_macs2_pooled_peaks.narrowPeak", mark=MARK),
-        E11 = expand("results/macs2/E11.5_{mark}_macs2_pooled_peaks.narrowPeak", mark=MARK),
-        E12 = expand("results/macs2/E12.5_{mark}_macs2_pooled_peaks.narrowPeak", mark=MARK),
-        E13 = expand("results/macs2/E13.5_{mark}_macs2_pooled_peaks.narrowPeak", mark=MARK),
-        E14 = expand("results/macs2/E14.5_{mark}_macs2_pooled_peaks.narrowPeak", mark=MARK),
-        E15 = expand("results/macs2/E15.5_{mark}_macs2_pooled_peaks.narrowPeak", mark=MARK)
-    run:
-        shell("cat {input.E10} | sort -k1,1 -k2,2n - | bedtools merge -i - > {output.E10}")
-        shell("cat {input.E11}| sort -k1,1 -k2,2n - | bedtools merge -i - > {output.E11}")
-        shell("cat {input.E12} | sort -k1,1 -k2,2n - | bedtools merge -i - > {output.E12}")
-        shell("cat {input.E13} | sort -k1,1 -k2,2n - | bedtools merge -i - > {output.E13}")
-        shell("cat {input.E14} | sort -k1,1 -k2,2n - | bedtools merge -i - > {output.E14}")
-        shell("cat {input.E15} | sort -k1,1 -k2,2n - | bedtools merge -i - > {output.E15}")
-
 rule overlap_peaks:
     input:
-        E10= expand(["results/macs2/{case}_vs_{control}_E10.5_{mark}_macs2_peaks.narrowPeak"], zip, case=IPS, control=INPUTS, mark=MARK),
-        E11= expand(["results/macs2/{case}_vs_{control}_E11.5_{mark}_macs2_peaks.narrowPeak"], zip, case=IPS, control=INPUTS, mark=MARK),
-        E12= expand(["results/macs2/{case}_vs_{control}_E12.5_{mark}_macs2_peaks.narrowPeak"], zip, case=IPS, control=INPUTS, mark=MARK),
-        E13= expand(["results/macs2/{case}_vs_{control}_E13.5_{mark}_macs2_peaks.narrowPeak"], zip, case=IPS, control=INPUTS, mark=MARK),
-        E14= expand(["results/macs2/{case}_vs_{control}_E14.5_{mark}_macs2_peaks.narrowPeak"], zip, case=IPS, control=INPUTS, mark=MARK),
-        E15= expand(["results/macs2/{case}_vs_{control}_E15.5_{mark}_macs2_peaks.narrowPeak"], zip, case=IPS, control=INPUTS, mark=MARK),
-        E10_pooled=expand("results/macs2/E10.5_{mark}_macs2_pooled_peaks.narrowPeak", mark=MARK),
-        E11_pooled=expand("results/macs2/E11.5_{mark}_macs2_pooled_peaks.narrowPeak", mark=MARK),
-        E12_pooled=expand("results/macs2/E12.5_{mark}_macs2_pooled_peaks.narrowPeak", mark=MARK),
-        E13_pooled=expand("results/macs2/E13.5_{mark}_macs2_pooled_peaks.narrowPeak", mark=MARK),
-        E14_pooled=expand("results/macs2/E14.5_{mark}_macs2_pooled_peaks.narrowPeak", mark=MARK),
-        E15_pooled=expand("results/macs2/E15.5_{mark}_macs2_pooled_peaks.narrowPeak", mark=MARK),
+        E10= expand(["results/macs2/{case}_vs_{control}_E10.5_H3K27ac_macs2_peaks.narrowPeak"], zip, case=IPS, control=INPUTS, mark=MARK),
+        E11= expand(["results/macs2/{case}_vs_{control}_E11.5_H3K27ac_macs2_peaks.narrowPeak"], zip, case=IPS, control=INPUTS, mark=MARK),
+        E12= expand(["results/macs2/{case}_vs_{control}_E12.5_H3K27ac_macs2_peaks.narrowPeak"], zip, case=IPS, control=INPUTS, mark=MARK),
+        E13= expand(["results/macs2/{case}_vs_{control}_E13.5_H3K27ac_macs2_peaks.narrowPeak"], zip, case=IPS, control=INPUTS, mark=MARK),
+        E14= expand(["results/macs2/{case}_vs_{control}_E14.5_H3K27ac_macs2_peaks.narrowPeak"], zip, case=IPS, control=INPUTS, mark=MARK),
+        E15= expand(["results/macs2/{case}_vs_{control}_E15.5_H3K27ac_macs2_peaks.narrowPeak"], zip, case=IPS, control=INPUTS, mark=MARK),
+        E10_pooled="results/macs2/E10.5_H3K27ac.pooled.macs2_peaks.narrowPeak",
+        E11_pooled="results/macs2/E11.5_H3K27ac.pooled.macs2_peaks.narrowPeak",
+        E12_pooled="results/macs2/E12.5_H3K27ac.pooled.macs2_peaks.narrowPeak",
+        E13_pooled="results/macs2/E13.5_H3K27ac.pooled.macs2_peaks.narrowPeak",
+        E14_pooled="results/macs2/E14.5_H3K27ac.pooled.macs2_peaks.narrowPeak",
+        E15_pooled="results/macs2/E15.5_H3K27ac.pooled.macs2_peaks.narrowPeak",
     output:
-        E10= expand("results/macs2/{mark}_E10.5_overlap.narrowPeak", mark=MARK),
-        E11= expand("results/macs2/{mark}_E11.5_overlap.narrowPeak", mark=MARK),
-        E12= expand("results/macs2/{mark}_E12.5_overlap.narrowPeak", mark=MARK),
-        E13= expand("results/macs2/{mark}_E13.5_overlap.narrowPeak", mark=MARK),
-        E14= expand("results/macs2/{mark}_E14.5_overlap.narrowPeak", mark=MARK),
-        E15= expand("results/macs2/{mark}_E15.5_overlap.narrowPeak", mark=MARK)
+        E10= "results/macs2/H3K27ac_E10.5_overlap.narrowPeak",
+        E11= "results/macs2/H3K27ac_E11.5_overlap.narrowPeak",
+        E12= "results/macs2/H3K27ac_E12.5_overlap.narrowPeak",
+        E13= "results/macs2/H3K27ac_E13.5_overlap.narrowPeak",
+        E14= "results/macs2/H3K27ac_E14.5_overlap.narrowPeak",
+        E15= "results/macs2/H3K27ac_E15.5_overlap.narrowPeak"
     run:
         shell("python2.7 scripts/overlap_peaks.py {input.E10} {input.E10_pooled} {output.E10}")
         shell("python2.7 scripts/overlap_peaks.py {input.E11} {input.E11_pooled} {output.E11}")