Mercurial > repos > guerler > springsuite

comparison spring_minz.py @ 11:21a7dd67b483 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit f208fb81425711754738fc8e612ee2d5cc26377f"
author guerler
date Fri, 25 Sep 2020 19:07:14 +0000
parents 4ac5d5a9b21c
children 4a4888bf0338
comparison
equal deleted inserted replaced
10:860bd6f8f480 11:21a7dd67b483
39 minz = score 39 minz = score
40 if minz > args.minscore: 40 if minz > args.minscore:
41 interactions.append((name, minz)) 41 interactions.append((name, minz))
42 print("Predicting: %s, min-Z: %s" % (name, minz)) 42 print("Predicting: %s, min-Z: %s" % (name, minz))
43 interactions.sort(key=lambda tup: tup[1], reverse=True) 43 interactions.sort(key=lambda tup: tup[1], reverse=True)
44 with open(args.output, 'w') as output_file: 44 with open(args.output, 'a+') as output_file:
45 for i in interactions: 45 for i in interactions:
46 output_file.write("%s %s\n" % (i[0], i[1])) 46 output_file.write("%s %s %s\n" % (args.name, i[0], i[1]))
47 47
48 def get_template_scores(hhr_file, min_score, identifier_length): 48 def get_template_scores(hhr_file, min_score, identifier_length):
49 result = {} 49 result = {}
50 identifier_length = identifier_length + 4 50 identifier_length = identifier_length + 4
51 if os.path.isfile(hhr_file): 51 if os.path.isfile(hhr_file):
61 return result 61 return result
62 62
63 if __name__ == "__main__": 63 if __name__ == "__main__":
64 parser = argparse.ArgumentParser(description='This script identifies interactions by detecting matching HH-search results.') 64 parser = argparse.ArgumentParser(description='This script identifies interactions by detecting matching HH-search results.')
65 parser.add_argument('-t', '--target', help='HHR target file result', required=True) 65 parser.add_argument('-t', '--target', help='HHR target file result', required=True)
66 parser.add_argument('-n', '--name', help='HHR target name', required=True)
66 parser.add_argument('-c', '--crossreference', help='Cross Reference index file', required=True) 67 parser.add_argument('-c', '--crossreference', help='Cross Reference index file', required=True)
67 parser.add_argument('-x', '--idx', help='Length of identifier', type=int, default=6) 68 parser.add_argument('-x', '--idx', help='Length of identifier', type=int, default=6)
68 parser.add_argument('-l', '--list', help='Text file containing identifiers.', required=True) 69 parser.add_argument('-l', '--list', help='Text file containing identifiers.', required=True)
69 parser.add_argument('-i', '--inputs', help='Directory containing `hhr` files', required=True) 70 parser.add_argument('-i', '--inputs', help='Directory containing `hhr` files', required=True)
70 parser.add_argument('-o', '--output', help='Output file containing minZ-scores`', required=True) 71 parser.add_argument('-o', '--output', help='Output file containing minZ-scores`', required=True)