def input_file_run(objs, infile, outfile, detail):
'''
Run TCSS when input file is provided.
'''
file = open(infile, 'r')
result = ""
for line in file:
line = line.strip().split(",")
if len(line) > 2:
print('File format not proper: refer README')
sys.exit()
result += calculate_semantic_similarity(objs, line[0], line[1], detail)
file.close()
output_results(result, outfile)
def input_file_run(objs, infile, outfile, detail):
'''
Run TCSS when input file is provided.
'''
file = open(infile, 'r')
result = ""
for line in file:
line = line.strip().split(",")
if len(line) > 2:
print 'File format not proper: refer README'
sys.exit()
result += calculate_semantic_similarity(objs, line[0], line[1], detail)
file.close()
output_results(result, outfile)
Output the results on screen or on file.
'''
if outfile:
try:
file = open(outfile, 'w')
file.write(result)
file.close()
except:
print(
"Cannot open output file: check path or permissions \n Printing results on screen"
)
print(result)
else:
print(result)
if __name__ == '__main__':
options = _command_line_arguments(sys.argv[1:])
objs = load_semantic_similarity(options['go'], options['gene'],
options['ontology'], options['drop'])
if options['input']:
input_file_run(objs, options['input'], options['output'],
options['detail'])
else:
result = calculate_semantic_similarity(objs, options['args'][0],
options['args'][1],
options['detail'])
output_results(result, options['output'])
def output_results(result, outfile):
'''
Output the results on screen or on file.
'''
if outfile:
try:
file = open(outfile, 'w')
file.write(result)
file.close()
except:
print "Cannot open output file: check path or permissions \n Printing results on screen"
print result
else:
print result
if __name__ == '__main__':
options = _command_line_arguments(sys.argv[1:])
objs = load_semantic_similarity(options['go'], options['gene'], options['ontology'], options['drop'])
if options['input']:
input_file_run(objs, options['input'], options['output'], options['detail'])
else:
result = calculate_semantic_similarity(objs, options['args'][0], options['args'][1], options['detail'])
output_results(result, options['output'])