def init():
global html_path
html_path = "../results"
global compound2smiles
compound2smiles = util.parse_dat("../metacyc/compounds.dat", "UNIQUE-ID",
"SMILES")
global atom_types
atom_types = ['C', 'N', 'O', 'P', 'S']
#global bond_types; bond_types = range(5)
global bond_types
bond_types = range(4)
global motif_sizes
motif_sizes = range(2, 7)
global log_zero
log_zero = -800.0
global compound2graph
compound2graph = {}
for compound in compound2smiles.keys():
try:
compound2graph[compound] = chemconvert.molfile2graph("../mol/" +
compound +
".mol")
except Exception:
pass
return
def convert_compounds_hash(compound_dat_filename):
compound2hash = util.parse_dat(compound_dat_filename, "UNIQUE-ID", "HASH")
util._mkdir("../mol")
for (key, smiles) in compound2hash.iteritems():
mol_filename = "../mol/" + key + ".mol"
if (not os.path.exists(mol_filename)):
print "Writing a MOL file to: " + mol_filename
if (len(smiles) > 0):
mol = chemconvert.hash2graph(smiles[0]).to_mol()
mol_file = open(mol_filename, "w")
mol_file.write(mol)
mol_file.close()
else:
print "Found the MOL file: " + mol_filename
return
def convert_compounds_hash(compound_dat_filename):
compound2hash = util.parse_dat(compound_dat_filename, "UNIQUE-ID", "HASH")
util._mkdir("../mol")
for (key, smiles) in compound2hash.iteritems():
mol_filename = "../mol/" + key + ".mol"
if (not os.path.exists(mol_filename)):
print "Writing a MOL file to: " + mol_filename
if (len(smiles) > 0):
mol = chemconvert.hash2graph(smiles[0]).to_mol()
mol_file = open(mol_filename, "w")
mol_file.write(mol)
mol_file.close()
else:
print "Found the MOL file: " + mol_filename
return
def main():
import argparse
parser = argparse.ArgumentParser()
parser.add_argument('identifier', help='Identifier name e.g. cne.100899.FST.')
parser.add_argument('-f', '--file', nargs='?', type=argparse.FileType('r'), default=sys.stdin,
help='Input file e.g. d2z.dat.')
parser.add_argument('--extra_data', type=argparse.FileType('r'), default='hg18.toDanRer5.seqs.txt',
help='Extra data file e.g. hg18.toDanRer5.seqs.txt.')
parser.add_argument('--valid', type=int, default=9, help='Field number of valid test coordinates.')
OPTS = parser.parse_args()
cne_dict = parse_dat(read_fields(f=OPTS.file))
line_tups = read_fields(f=OPTS.extra_data)
cne_valids = {}
for l in line_tups:
danrer_co, valid_co = parse_coords(l[4]), parse_coords(l[OPTS.valid-1])
valid_indices = (valid_co['start'] - danrer_co['start'], valid_co['end'] - danrer_co['start'])
cne_valids[l[0]] = valid_indices
plot_cne(OPTS.identifier, cne_dict[OPTS.identifier], cne_valids[OPTS.identifier])
def main():
import argparse
parser = argparse.ArgumentParser()
parser.add_argument('-f', '--file', nargs='?', type=argparse.FileType('r'), default=sys.stdin,
help='Input file e.g. d2z.dat.')
parser.add_argument('--extra_data', type=argparse.FileType('r'), default='hg18.toDanRer5.seqs.txt',
help='Extra data file e.g. hg18.toDanRer5.seqs.txt.')
parser.add_argument('scoring', choices=['ranked_peaks', 'overlap'])
OPTS = parser.parse_args()
line_tups = read_fields(f=OPTS.file)
cne_dict = parse_dat(line_tups)
extra = parse_extra_data(read_fields(f=OPTS.extra_data))
if OPTS.scoring == 'ranked_peaks':
results = ranked_peaks(cne_dict, extra)
elif OPTS.scoring == 'overlap':
results = overlap(cne_dict, extra)
for cne, result in sorted(results.iteritems()):
sys.stdout.write('\t'.join([cne, str(result['rank']),
str(result['places'])]) + '\n')
def init():
global html_path; html_path = "../results"
global compound2smiles;
compound2smiles = util.parse_dat("../metacyc/compounds.dat", "UNIQUE-ID", "SMILES")
global atom_types; atom_types = ['C', 'N', 'O', 'P', 'S']
#global bond_types; bond_types = range(5)
global bond_types; bond_types = range(4)
global motif_sizes; motif_sizes = range(2, 7)
global log_zero; log_zero = -800.0
global compound2graph; compound2graph = {}
for compound in compound2smiles.keys():
try:
compound2graph[compound] = chemconvert.molfile2graph("../mol/" + compound + ".mol")
except Exception:
pass
return
