annotate spring_minz.py @ 16:16eb2acaaa20 draft

"planemo upload commit 0e4e1f8de9464b411152c44f4edd099db8ad9e0b"

#! /usr/bin/env python3
import argparse
import os

def main(args):
	names = []
	with open(args.list) as file:
		for index, line in enumerate(file):
			names.append(line.strip())
	print ("Loaded %s names from `%s`." % (len(names), args.list))
	crossreference = {}
	with open(args.crossreference) as file:
		for index, line in enumerate(file):
			columns = line.split()
			core = columns[0]
			partner = columns[-1]
			if core not in crossreference:
				crossreference[core] = []
			crossreference[core].append(partner)
	print ("Loaded cross reference from `%s`." % args.crossreference)
	toptarget, 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)
			toptemplate, templates = get_template_scores(input_file, args.minscore, args.idx)
			minz = 0
			mint = ""
			for t in targets:
				if t in crossreference:
					partners = crossreference[t]
					for p in partners:
						if p in templates:
							score = min(targets[t], templates[p])
							if score > minz:
								minz = score
								mint = "%s\t%s\t%s\t%s" % (toptarget, toptemplate, t, p)
			if minz > args.minscore:
				interactions.append((name, minz, mint))
				print("Predicting: %s, min-Z: %s, templates: %s" % (name, minz, mint))
		interactions.sort(key=lambda tup: tup[1], reverse=True)
	with open(args.output, 'a+') as output_file:
		for i in interactions:
			output_file.write("%s\t%s\t%s\t%s\n" % (args.name, i[0], i[1], i[2]))

def get_template_scores(hhr_file, min_score, identifier_length):
	result = {}
	toptemplate = None
	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:
						if toptemplate is None:
							toptemplate = template_id
						result[template_id] = template_score
	return toptemplate, 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('-n', '--name', help='HHR target name', 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 min-Z scores`', required=True)
	parser.add_argument('-m', '--minscore', help='min-Z score threshold', type=int, default=10)
	args = parser.parse_args()
	main(args)