def testStr(self):
"""Test if we can convert each record to a string correctly"""
f = open(self.filename)
try:
for line in f:
record = Cla.Record(line)
# The SCOP Classification file format which can be found at
# http://scop.mrc-lmb.cam.ac.uk/scop/release-notes.html states
# that the list of classification hierarchy key-value pairs is
# unordered, therefore we need only check that they are all
# there, NOT that they are in the same order.
#End of line is platform dependent. Strip it off
expected_hierarchy = line.rstrip().split('\t')[5].split(',')
expected_hierarchy = dict(
pair.split('=') for pair in expected_hierarchy)
actual_hierarchy = str(record).rstrip().split('\t')[5].split(
',')
actual_hierarchy = dict(
pair.split('=') for pair in actual_hierarchy)
self.assertEqual(len(actual_hierarchy),
len(expected_hierarchy))
for key, actual_value in actual_hierarchy.iteritems():
self.assertEqual(actual_value, expected_hierarchy[key])
finally:
f.close()
def testParse(self):
"""Test if all records in a CLA file are being read."""
count = 0
with open(self.filename) as f:
records = Cla.parse(f)
for record in records:
count += 1
self.assertEqual(count, 14)
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 testError(self) :
corruptRec = "49268\tsp\tb.1.2.1\t-\n"
try:
record = Cla.Record(corruptRec)
assert False, "Should never get here"
except ValueError, e :
pass
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 testStr(self):
f = open(self.filename)
try:
for line in f:
record = Cla.Record(line)
#End of line is platform dependent. Strip it off
assert str(record).rstrip() == line.rstrip()
finally:
f.close()
def testParse(self):
"""Test if all records in a CLA file are being read"""
f=open(self.filename)
try:
count = 0
records = Cla.parse(f)
for record in records:
count +=1
self.assertEqual(count, 14)
finally:
f.close()
def testParse(self):
"""Can we parse a CLA file?"""
f=open(self.filename)
try:
count = 0
records = Cla.parse(f)
for record in records:
count +=1
assert count == 14, "Wrong number of records?!"
finally:
f.close()
def testParse(self):
"""Test if all records in a CLA file are being read"""
f = open(self.filename)
try:
count = 0
records = Cla.parse(f)
for record in records:
count += 1
self.assertEqual(count, 14)
finally:
f.close()
def testParse(self):
"""Can we parse a CLA file?"""
f=open(self.filename)
try:
count = 0
records = Cla.parse(f)
for record in records:
count +=1
assert count == 14, "Wrong number of records?!"
finally:
f.close()
def testRecord(self) :
recLine = 'd1dan.1\t1dan\tT:,U:91-106\tb.1.2.1\t21953\tcl=48724,cf=48725,sf=49265,fa=49266,dm=49267,sp=49268,px=21953'
record = Cla.Record(recLine)
assert record.sid =='d1dan.1'
assert record.residues.pdbid =='1dan'
assert record.residues.fragments ==(('T','',''),('U','91','106'))
assert record.sccs == 'b.1.2.1'
assert record.sunid == 21953
assert record.hierarchy == [['cl',48724],['cf',48725],['sf',49265],
['fa',49266],['dm',49267],['sp',49268],
['px',21953]], record.hierarchy
def testRecord(self):
"""Test one record in detail"""
recLine = 'd1dan.1\t1dan\tT:,U:91-106\tb.1.2.1\t21953\tcl=48724,cf=48725,sf=49265,fa=49266,dm=49267,sp=49268,px=21953'
record = Cla.Record(recLine)
self.assertEqual(record.sid, 'd1dan.1')
self.assertEqual(record.residues.pdbid, '1dan')
self.assertEqual(record.residues.fragments, (('T','',''),('U','91','106')))
self.assertEqual(record.sccs, 'b.1.2.1')
self.assertEqual(record.sunid, 21953)
self.assertEqual(record.hierarchy, {'cl' : 48724,
'cf' : 48725,
'sf' : 49265,
'fa' : 49266,
'dm' : 49267,
'sp' : 49268,
'px' : 21953})
def testRecord(self):
"""Test one record in detail."""
recLine = "d1dan.1\t1dan\tT:,U:91-106\tb.1.2.1\t21953\tcl=48724,cf=48725,sf=49265,fa=49266,dm=49267,sp=49268,px=21953"
record = Cla.Record(recLine)
self.assertEqual(record.sid, "d1dan.1")
self.assertEqual(record.residues.pdbid, "1dan")
self.assertEqual(record.residues.fragments,
(("T", "", ""), ("U", "91", "106")))
self.assertEqual(record.sccs, "b.1.2.1")
self.assertEqual(record.sunid, 21953)
self.assertEqual(
record.hierarchy, {
"cl": 48724,
"cf": 48725,
"sf": 49265,
"fa": 49266,
"dm": 49267,
"sp": 49268,
"px": 21953
})
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()