parallel upstream and downstream marker per chromosome

rules/bedtoolsClosest.smk

@@ -41,12 +41,18 @@ rule downstreamClosest:
 		bedtools closest -k 5 -iu -D ref -io -a {input.annot} -b {input.markers} 1> {output} 2> {log}
 		"""
 
-# rule mergeClosest:
-# 	message: " Merge both upstream and downstream results"
-# 	input: up=config['results']+'/2.closestbedUpstream.txt', down=config['results']+'/2.downstreamClosest.txt'
-# 	output: config['results']+'/2.mergedClosestMarkers.txt'
-# 	log: config['results']+'/2.mergedClosestMarkers.log'
-# 	shell:
-# 		"""
-# 		join -1 4 -2 4 <(sort -k4,4 {input.up}) <(sort -k4,4 {input.down})|sed "s/ /\t/g"|cut -f -11,17- |sort -k2,2 -k3,3n |awk "{{size=\$14-\$8;print \$0,size}}"|sed "s/ /\t/g" 1> {output} 2> {log}
-# 		"""
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+rule splitPerChrom:
+	message: "Split data per chromosome"
+	input: 
+		upstream=config['results']+'/2.closestbedUpstream.txt',
+		downstream=config['results']+'/2.downstreamClosest.txt'
+	output:
+		splitUp=config['results']+'/2.closestbed_split/{chrom}.upstream.txt',
+		splitDown=config['results']+'/2.closestbed_split/{chrom}.downstream.txt'
+	params: chromPref='TraesCS{chrom}'
+	log: config['results']+'/2.closestbed_split/{chrom}.split.log'
+	shell:
+		"""
+		fgrep -w {params.chromPref} {input.upstream} 1> {output.splitUp} 2> {log}
+		fgrep -w {params.chromPref} {input.downstream} 1> {output.splitDown} 2>> {log}
+		"""
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