Script to parse the output of script to merge SVs and create a table mapping segments to GROUP ID

utils/create-sv-group-track.py

+#!/usr/bin/env python
+
+import sys
+from argparse import ArgumentParser
+import pandas as pd
+import re
+
+def parse_position(s):
+	r = re.compile('(chr.*):([0-9\\.e\\+]+)-([0-9\\.e\\+]+)')
+	chrom, start, end = r.fullmatch(s).groups()
+	return chrom, int(float(start)), int(float(end))
+
+
+def main():
+	parser = ArgumentParser(prog='create-sv-group-track.py', description=__doc__)
+
+	parser.add_argument('mergetable', metavar='TABLE', help='Table as output by group_nearby_calls_of_same_AF_and_generate_output_table.pl')
+
+	args = parser.parse_args()
+
+	print('Reading', args.mergetable, file=sys.stderr)
+	table = pd.read_csv(args.mergetable, sep=', ', engine='python')
+
+	print('chrom', 'start', 'end', 'group_id', sep='\t')
+	r = re.compile('\\[Group_([0-9]+)/(.*)\\]')
+	for x in table['segments'].values:
+		m = r.fullmatch(x)
+		if m is None:
+			continue
+		group_id, position_list = m.groups()
+		for chrom, start, end in (parse_position(p) for p in position_list.split('|')):
+			print(chrom, start, end, group_id, sep='\t')
+
+
+if __name__ == '__main__':
+	main()