def testIndex(self) :
index = Cla.Index(self.filename)
assert len(index)==14
assert index.has_key('d4hbia_')
rec = index['d1hbia_']
assert rec.sunid == 14996
def testIndex(self):
"""Test CLA file indexing."""
index = Cla.Index(self.filename)
self.assertEqual(len(index), 14)
self.assertIn("d4hbia_", index)
rec = index["d1hbia_"]
self.assertEqual(rec.sunid, 14996)
def testIndex(self):
"""Test CLA file indexing"""
index = Cla.Index(self.filename)
self.assertEqual(len(index), 14)
self.assertTrue('d4hbia_' in index)
rec = index['d1hbia_']
self.assertEqual(rec.sunid, 14996)
def main():
try:
opts, args = getopt.getopt(
sys.argv[1:], "hp:o:i:",
["help", "usage", "pdb=", "output=", "input="])
except getopt.GetoptError:
# show help information and exit:
usage()
sys.exit(2)
input = None
in_handle = None
output = None
pdb_url = None
cla_url = None
raf_url = None
for o, a in opts:
if o in ("-h", "--help", "--usage"):
usage()
sys.exit()
elif o in ("-o", "--output"):
output = a
elif o in ("-i", "--input"):
input = a
elif o in ("-p", "--pdb"):
pdb_url = a
if len(args) < 2:
sys.stderr.write(
"Not enough arguments. Try --help for more details.\n")
sys.exit(2)
raf_url = args[0]
cla_url = args[1]
(raf_filename, headers) = _urlretrieve(raf_url)
seqMapIndex = Raf.SeqMapIndex(raf_filename)
(cla_filename, headers) = _urlretrieve(cla_url)
claIndex = Cla.Index(cla_filename)
if input is None:
sids = args[2:]
elif input == '-':
sids = sys.stdin
else:
in_handle = open(input)
sids = in_handle
try:
for sid in sids:
if not sid or sid[0:1] == '#':
continue
id = sid[0:7]
pdbid = id[1:5]
s = pdbid[0:1]
if s == '0' or s == 's':
sys.stderr.write("No coordinates for domain %s\n" % id)
continue
if output is None:
filename = id + ".ent"
out_handle = open(filename, "w+")
elif output == '-':
out_handle = sys.stdout
else:
out_handle = open(output, "w+")
try:
try:
claRec = claIndex[id]
residues = claRec.residues
seqMap = seqMapIndex.getSeqMap(residues)
pdbid = residues.pdbid
f = open_pdb(pdbid, pdb_url)
try:
seqMap.getAtoms(f, out_handle)
finally:
f.close()
except (IOError, KeyError, RuntimeError) as e:
sys.stderr.write("I cannot do SCOP domain %s : %s\n" %
(id, e))
finally:
out_handle.close()
finally:
if in_handle is not None:
in_handle.close()
