comparison spring_minz.py @ 9:4ac5d5a9b21c draft

"planemo upload commit f465445ebca0307953f59938494a2244ca8ea23c"

8:f2f38991c36f

			partner = columns[2]
			if core not in crossreference:
				crossreference[core] = []
			crossreference[core].append(partner)
	print ("Loaded cross reference from `%s`." % args.crossreference)
	targets = get_template_scores(args.target, args.minscore)
	interactions = []
	if not targets:
		print("No targets found `%s`" % args.target)
	else:
		print ("Loaded target scores from `%s`." % args.target)
		for name in names:
			input_directory = args.inputs.rstrip("/")
			input_file = "%s/%s" % (input_directory, name)
			templates = get_template_scores(input_file, args.minscore)
			minz = 0
			for t in targets:
				if t in crossreference:
					partners = crossreference[t]
					for p in partners:

		interactions.sort(key=lambda tup: tup[1], reverse=True)
	with open(args.output, 'w') as output_file:
		for i in interactions:
			output_file.write("%s %s\n" % (i[0], i[1]))

def get_template_scores(hhr_file, min_score):
	result = {}
	if os.path.isfile(hhr_file):
		with open(hhr_file) as file:
			for index, line in enumerate(file):
				if index > 8:
					if not line.strip():
						break
					template_id = line[4:10]
					template_score = float(line[57:63])
					if template_score > min_score:
						result[template_id] = template_score
	return result

if __name__ == "__main__":
	parser = argparse.ArgumentParser(description='This script identifies interactions by detecting matching HH-search results.')
	parser.add_argument('-t', '--target', help='HHR target file result', required=True)
	parser.add_argument('-c', '--crossreference', help='Cross Reference index file', required=True)
	parser.add_argument('-l', '--list', help='Text file containing identifiers.', required=True)
	parser.add_argument('-i', '--inputs', help='Directory containing `hhr/X/Y.hhr` files', required=True)
	parser.add_argument('-o', '--output', help='Output file containing minZ-scores`', required=True)
	parser.add_argument('-m', '--minscore', help='min-Z score threshold', type=int, default=10)
	args = parser.parse_args()
	main(args)

9:4ac5d5a9b21c

			partner = columns[2]
			if core not in crossreference:
				crossreference[core] = []
			crossreference[core].append(partner)
	print ("Loaded cross reference from `%s`." % args.crossreference)
	targets = get_template_scores(args.target, args.minscore, args.idx)
	interactions = []
	if not targets:
		print("No targets found `%s`" % args.target)
	else:
		print ("Loaded target scores from `%s`." % args.target)
		for name in names:
			input_directory = args.inputs.rstrip("/")
			input_file = "%s/%s" % (input_directory, name)
			templates = get_template_scores(input_file, args.minscore, args.idx)
			minz = 0
			for t in targets:
				if t in crossreference:
					partners = crossreference[t]
					for p in partners:

		interactions.sort(key=lambda tup: tup[1], reverse=True)
	with open(args.output, 'w') as output_file:
		for i in interactions:
			output_file.write("%s %s\n" % (i[0], i[1]))

def get_template_scores(hhr_file, min_score, identifier_length):
	result = {}
	identifier_length = identifier_length + 4
	if os.path.isfile(hhr_file):
		with open(hhr_file) as file:
			for index, line in enumerate(file):
				if index > 8:
					if not line.strip():
						break
					template_id = line[4:identifier_length]
					template_score = float(line[57:63])
					if template_score > min_score:
						result[template_id] = template_score
	return result

if __name__ == "__main__":
	parser = argparse.ArgumentParser(description='This script identifies interactions by detecting matching HH-search results.')
	parser.add_argument('-t', '--target', help='HHR target file result', required=True)
	parser.add_argument('-c', '--crossreference', help='Cross Reference index file', required=True)
	parser.add_argument('-x', '--idx', help='Length of identifier', type=int, default=6)
	parser.add_argument('-l', '--list', help='Text file containing identifiers.', required=True)
	parser.add_argument('-i', '--inputs', help='Directory containing `hhr` files', required=True)
	parser.add_argument('-o', '--output', help='Output file containing minZ-scores`', required=True)
	parser.add_argument('-m', '--minscore', help='min-Z score threshold', type=int, default=10)
	args = parser.parse_args()
	main(args)