CNV consensus (3 of n): Filter bad segments

analyses/copy_number_consensus_call/Snakefile

@@ -2,15 +2,17 @@
 # Updated Dec 5, 2019
 
 ## Define the ending file(s) that we want
-ALL_FREEC= expand("../../scratch/interim/{sample}.freec.dup.bed", sample=config["samples"])
-ALL_CNVKIT= expand("../../scratch/interim/{sample}.cnvkit.dup.bed", sample=config["samples"])
-ALL_MANTA= expand("../../scratch/interim/{sample}.manta.dup.bed", sample=config["samples"])
+ALL_FREEC= expand("../../scratch/interim/{sample}.freec.dup.filtered.bed", sample=config["samples"])
+ALL_CNVKIT= expand("../../scratch/interim/{sample}.cnvkit.dup.filtered.bed", sample=config["samples"])
+OUTPUT= expand("../../scratch/interim/{sample}.{caller}.dup.filtered.bed", 
+               sample=config["samples"], 
+               caller=["freec", "cnvkit", "manta"])
 
 
 ## Define the first rule of the Snakefile. This rule determines what the final file is and which steps to be taken.
 rule all:
     input:
-        ALL_FREEC + ALL_CNVKIT + ALL_MANTA
+        OUTPUT
 
 
 #########################      FILTER STEP FOR THE 3 CALL METHODS ####################################
@@ -83,3 +85,22 @@ rule manta_filter:
         """ | sort -k1,1 -k2,2n > {output.manta_del} && """
         """awk '$6~/DUP/ {{if ($5 > {params.SIZE_CUTOFF}) {{print$2,$3,$4,$5,"NA","NA",$6}}}}' {input} """
         """ | sort -k1,1 -k2,2n > {output.manta_dup}"""
+
+
+rule filter_telomeres:
+    input:
+        ## Define the location of the input file and take the path/extension from the config file
+        script=os.path.join(config["scripts"], "get_rid_bad_segments.py"),
+        bad_list=os.path.join(config["scripts"], "bad_chromosomal_seg_updated_merged.txt"),
+        bedfile="../../scratch/interim/{sample}.{caller}.{dupdel}.bed"
+    output:
+        ## Define the output files' names
+        filtered_bed="../../scratch/interim/{sample}.{caller}.{dupdel}.filtered.bed"
+    wildcard_constraints:
+        caller = "cnvkit|freec|manta",
+        dupdel = "del|dup"
+    threads: 1
+    shell:
+        ## Invoke the python3 script and pass in the reference and CNVs files. Direct the stdout to a new file. 
+        "python3 {input.script} --reference {input.bad_list} --file {input.bedfile} > {output.filtered_bed}"
+