diff parse_strelka_makefile.py @ 0:88141dfd5db1 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/parse_strelka_makefile.py	Thu Aug 18 19:34:55 2016 -0400
@@ -0,0 +1,82 @@
+import argparse
+import sys
+import re
+
+if __name__ == '__main__':
+
+	desc = "Convert Strelka Makefile into a sub-Makefile used STRICTLY for parallelization by chromosome in Galaxy"
+	parser = argparse.ArgumentParser(description=desc)
+	parser.add_argument(
+		"-m", "--makefile",
+		required=True,
+		help="Input Must be a Strelka Makefile"
+		)
+	parser.add_argument(
+		"-c", "--chrom",
+		type=str,
+		required=False,
+		help="Chromosome present in the Strelka Makefile"
+		)
+	parser.add_argument(
+		"-cf", "--chrom_file",
+		required=False,
+		help="Chromosome File separated by newline"
+		)
+	parser.add_argument(
+		'-o', '--output',
+		required=True,
+		help="Output Makefile"
+		)
+	args = parser.parse_args()
+
+	if (not args.chrom and not args.chrom_file) or (args.chrom and args.chrom_file):
+		sys.exit('Must define a single chromosome entry or a single chromosome file')
+
+	chromosomes = [];
+
+	if args.chrom_file:
+		chromosomes = open(args.chrom_file).read().splitlines()
+
+	if args.chrom:
+		chromosomes = [args.chrom]
+	add_at_end = []
+	makefile_in = open(args.makefile, 'r')
+	makefile_out = open(args.output, 'w')
+
+	for line in makefile_in:
+		if line.startswith('script_dir'):
+			makefile_out.write(line)
+		elif line.startswith('call_script'):
+			makefile_out.write(line)		
+		elif line.startswith('filter_script'):
+			makefile_out.write(line)
+		elif line.startswith('finish_script'):
+			makefile_out.write(line)
+		elif line.startswith('script_dir'):
+			makefile_out.write(line)
+		elif line.startswith('config_file'):
+			makefile_out.write(line)
+		elif line.startswith('analysis_dir'):
+			makefile_out.write(line)
+		elif line.startswith('results_dir'):
+			makefile_out.write(line)		
+		elif line.startswith('get_chrom_dir'):
+			makefile_out.write(line)
+		elif line.startswith('get_chrom_task'):
+			makefile_out.write(line)
+		elif line.startswith('get_bin_task'):
+			makefile_out.write(line)
+			makefile_out.write('\n')
+		elif line.startswith('all:'):
+			makefile_out.write('all:\n')
+		elif re.search("--chrom=", line):
+			if re.search(''.join(["\s|".join(chromosomes),'\s']), line):
+				if re.search('bin', line):
+					makefile_out.write(line)
+				else:
+					add_at_end.append(line)
+
+	makefile_in.close()
+	for line in add_at_end:
+		makefile_out.write(line)
+	makefile_out.close()