def main():
from hpf.superfunc.go import read_file, output_matrix, output_sparse_matrix
print "Reading MGI IDs ({0}) and GO terms ({1}) for matrix creation".format(args.mgi_file, args.go_file)
mgi_ids = read_file(args.mgi_file)
go_terms = read_file(args.go_file)
print "Creating annotation matrix against database {0}".format(args.database)
annotation_matrix = build_annotation_matrix(mgi_ids, go_terms, args.database)
print "Writing annotation matrix to file {0}".format(args.outfile)
if args.store_sparse:
output_sparse_matrix(annotation_matrix, args.outfile, val=1)
else:
output_matrix(annotation_matrix, args.outfile)
def main():
from hpf.superfunc.go import read_file, output_matrix, output_sparse_matrix
print "Reading GO terms from infile {0}".format(args.go_file)
go_terms = read_file(args.go_file)
if args.type == "parent":
print "Building parent matrix against database {0}".format(args.database)
result_matrix = build_parent_matrix(go_terms, args.database)
elif args.type == "common_parent":
print "Building common parents matrix against database {0}".format(args.database)
result_matrix = build_common_parent_matrix(go_terms, args.database)
print "Writing parent matrix to file {0}".format(args.outfile)
if args.store_sparse:
output_sparse_matrix(result_matrix, args.outfile, val=1)
else:
output_matrix(result_matrix, args.outfile)