QCTable NReads Fix

Results-template/Scripts/filterMetrics

@@ -44,6 +44,8 @@ import sys
 def add(i1, i2):
 	return int(i1) + int(i2)
 
+def divide(num):
+	return int(num/4.0)
 
 def getmetadata(type):
 	metadata = []
@@ -54,11 +56,11 @@ def getmetadata(type):
 	elif type == 'nrf':
 		metadata = ["NRF", "PBC1", "PBC2"]
 	elif type == 'tnreads':
-		metadata = 'NumberofReads'
+		metadata = 'NReads'
 	elif type == 'mnreads':
-                metadata = 'NumberofMappedReads'
+                metadata = 'NMappedReads'
 	elif type == 'unreads':
-                metadata = 'NumberofUniquelyMappedReads'
+                metadata = 'NUniqMappedReads'
 	return metadata	
 
 
@@ -67,8 +69,12 @@ def filteredData(sample, ftype):
 		linelist = line.strip().split()
 		if 'reads' in ftype:
 			mtypes = getmetadata(ftype)
-			v1, v2 = linelist[0], linelist[1]
-			print("{}\t{}\t{}".format(sample, mtypes, add(v1,v2)))
+			if ftype == 'tnreads':
+				v1 = int(linelist[0])
+				print("{}\t{}\t{}".format(sample, mtypes, divide(v1)))
+			else:
+				v1, v2 = linelist[0], linelist[1]
+				print("{}\t{}\t{}".format(sample, mtypes, add(v1,v2)))
 		elif ftype == 'ppqt' or ftype == 'ngsqc' or ftype == 'nrf':
 			mtypes = getmetadata(ftype)
 			for i in range(len(linelist)):

Rules/InitialChIPseqQC.snakefile

@@ -774,6 +774,7 @@ python {params.nrfscript} {output.preseqlog} > {output.nrf}
 rule QCstats:
     input:
         flagstat=join(workpath,bam_dir,"{name}.sorted.bam.flagstat"),
+	infq=join(workpath,"{name}.R1.fastq.gz"),	
         ddflagstat=join(workpath,bam_dir,"{name}.sorted.Q5DD.bam.flagstat"),
         nrf=join(workpath,"QC","{name}.nrf"),
         ppqt=join(workpath,bam_dir,"{name}.sorted.Q5DD.ppqt"),
@@ -786,7 +787,8 @@ rule QCstats:
     threads: 16
     shell: """
 # Number of reads
-grep 'in total' {input.flagstat} | awk '{{print $1,$3}}' | {params.filterCollate} {wildcards.name} tnreads > {output.sampleQCfile}
+#grep 'in total' {input.flagstat} | awk '{{print $1,$3}}' | {params.filterCollate} {wildcards.name} tnreads > {output.sampleQCfile}
+zcat {input.infq} | wc -l | {params.filterCollate} {wildcards.name} tnreads > {output.sampleQCfile}
 # Number of mapped reads
 grep 'mapped (' {input.flagstat} | awk '{{print $1,$3}}' | {params.filterCollate} {wildcards.name} mnreads >> {output.sampleQCfile}
 # Number of uniquely mapped reads