# HG changeset patch
# User geoffrey.dintilhac
# Date 1576951010 18000
# Node ID 68f7b5a4b1e2c7f6cb00d68f5b264fa37c96a565

Uploaded

diff -r 000000000000 -r 68f7b5a4b1e2 bamtobed.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bamtobed.py	Sat Dec 21 12:56:50 2019 -0500
@@ -0,0 +1,55 @@
+#!/usr/bin/env python
+
+import argparse
+import os
+
+parser = argparse.ArgumentParser(description='Call bamtobed with parameters')
+parser.add_argument('-i', '--inputBAM', required=True, help='input BAM file')
+parser.add_argument('-o', '--outputBED', required=True, help='output BED file')
+parser.add_argument('-oot', '--otherOutputType', required=True, help='Y or N')
+parser.add_argument('-f', '--outputFormat', required=False, help='output file format')
+parser.add_argument('-sc', '--scoreCalculation', required=True, help='calculation for BED score')
+parser.add_argument('-tag', '--tag', required=False, help='another tag')
+parser.add_argument('-spt', '--splitD', required=False, help='split : with "N" CIGAR and "D" operation', action="store_true")
+parser.add_argument('-cgr', '--cigar', required=False, help='cigar string', action="store_true")
+
+args = parser.parse_args()
+
+# Displays the other output format if selected.
+if args.otherOutputType == "Y":
+	print('format output chosen : ' + args.outputFormat)
+
+# Construction of the command line calling the tool. 
+myCommandLine = ('bedtools bamtobed'+' -i ' + args.inputBAM)
+
+# Other output format options.
+if args.otherOutputType == "Y":
+	if args.outputFormat == "BEDPE":
+		myCommandLine += (' -bedpe ')
+	elif args.outputFormat == "BED12":
+		myCommandLine += (' -bed12 ')
+
+# Score calculation options.
+if args.scoreCalculation == "ed":
+	myCommandLine += (' -ed ')
+elif args.scoreCalculation == "tag":
+	myCommandLine += (' -tag ' + args.tag)
+
+# Split option.
+if args.splitD:
+	myCommandLine += (' -splitD ')
+	print('Splitted BAM')
+
+# CIGAR option.
+if args.cigar:
+	myCommandLine += (' -cigar ')
+	print('CIGAR string column added')
+
+myCommandLine += (' > ' + args.outputBED)
+
+# Running of the command line.
+os.system(myCommandLine)
+
+
+
+