Add script performance/add_sym_to_DepthOfCoverage.py

Author: jiaan-yu

performance/add_sym_to_DepthOfCoverage.py

@@ -0,0 +1,41 @@
+#!/usr/bin/python3
+
+"""
+Title: addSymToDepthOfCoverage.py
+Creator: Jason Li
+Updated: Jiaan Yu
+Date: 09-04-2020
+
+Annotate gene to Gatk3 DepthOfCoverage interval_summary output
+USAGE: 
+    addSymToDepthOfCoverage.py -i <DepthOfCoverageOut> -b <annotatedBed> -o <annotatedDepthOfCoverageResult>
+
+"""
+
+import argparse
+
+parser = argparse.ArgumentParser(description="Performance summary of bam")
+parser.add_argument("-i", help="Gatk3 DepthOfCoverage interval_summary output", metavar = "INPUT", required=True)
+parser.add_argument("-o", help="Output file name", metavar = "OUTPUT", required=True)
+parser.add_argument("-bed", help="Annotated bed file", metavar = "BED", required=True)
+args = parser.parse_args()
+
+
+geneDict = {}
+with open(args.bed, 'r') as bed_fh:
+    for line in bed_fh:
+        line_elems = line.rstrip("\n\r").split("\t")
+        var_id = "%s:%d-%s" % (line_elems[0], int(line_elems[1])+1, line_elems[2])
+        geneDict[var_id] = line_elems[3]
+
+fh = open(args.i)
+foh = open(args.o, 'w')
+foh.write("GeneSym\t" + fh.readline())
+for line in fh:
+    line_elems = line.rstrip("\n\r").split("\t")
+    var_id = line_elems[0]
+    gene = geneDict[var_id]
+    lineout = gene+"\t"+line
+    foh.write(lineout)
+fh.close()
+foh.close()