def __init__(self, value, type, id, residues=('???','???'), max=None, \
error=0.0):
from Mara.Library import omniTranslator
self.value = float(value)
self.__id__ = int(id)
if type is str and DCouplings.has_key(type):
self.__type__ = DCouplings[type]
elif isinstance(type, DCoupling):
self.__type__ = type
else:
raise TypeError, "Incompatible coupling type '%s'." % repr(type)
if (isinstance(residues, tuple) or isinstance(residues, list)) \
and len(residues) == 2 and \
isinstance(residues[0], str) and isinstance(residues[1], str):
self.residues = (omniTranslator(residues[0],
'3-letter-aminoacids'),
omniTranslator(residues[1],
'3-letter-aminoacids'))
else:
raise TypeError, "Incompatible residue names '%s'." % repr(
residues)
self.error = float(error)
self.tag = (self.__id__, str(self.__type__))
if max:
self.__max__ = float(max)
else:
self.__max__ = None
self.__name__ = 'Coupling'
def __init__(self, value, type, id, residues=('???','???'), max=None, \
error=0.0):
from Mara.Library import omniTranslator
self.value = float(value)
self.__id__ = int(id)
if type is str and DCouplings.has_key(type):
self.__type__ = DCouplings[type]
elif isinstance(type, DCoupling):
self.__type__ = type
else:
raise TypeError, "Incompatible coupling type '%s'." % repr(type)
if (isinstance(residues, tuple) or isinstance(residues, list)) \
and len(residues) == 2 and \
isinstance(residues[0], str) and isinstance(residues[1], str):
self.residues = (
omniTranslator(residues[0], '3-letter-aminoacids'),
omniTranslator(residues[1], '3-letter-aminoacids'))
else:
raise TypeError, "Incompatible residue names '%s'." % repr(residues)
self.error = float(error)
self.tag = (self.__id__, str(self.__type__))
if max:
self.__max__ = float(max)
else:
self.__max__ = None
self.__name__ = 'Coupling'
def getSequence(self, format='3-letter-aminoacids'):
if not omniTranslator.recognise_language(format):
raise ValueError, "Unknown format '%s'." % repr(format)
sequence = []
for residue in self:
name = omniTranslator(str(residue), format)
sequence.append(name)
return sequence
def getSequence(self, format='3-letter-aminoacids'):
if not omniTranslator.recognise_language(format):
raise ValueError, "Unknown format '%s'." % repr(format)
sequence = []
for residue in self:
name = omniTranslator(str(residue), format)
sequence.append(name)
return sequence
def write_sequence(seq, output=None, format='long', use_translator=True):
"""
Write amino acid sequence in the desired format either to a stream
given or to STDOUT.
TODO: - add some flexibility to the output formats
"""
if output is None:
output = sys.stdout
if format == 'long':
l = []
while seq:
s = seq.pop(0)
if use_translator:
s = omniTranslator(s.capitalize(), '3-letter-aminoacids')
l.append(s.upper())
if len(l) == 15:
output.write(' '.join(l) + '\n')
l = []
output.write(' '.join(l) + '\n')
elif format == 'full':
l = []
while seq:
s = seq.pop(0)
if use_translator:
s = omniTranslator(s.capitalize(), 'english')
l.append(s)
output.write(' '.join(l) + '\n')
else:
l = []
w = ''
while seq:
s = seq.pop(0)
if use_translator:
s = omniTranslator(s.capitalize(), '1-letter-aminoacids')
w += s.upper()
if len(w) == 10:
l.append(w)
w = ''
if len(l) == 6:
output.write(' '.join(l) + '\n')
l = []
if w:
l.append(w)
output.write(' '.join(l) + '\n')
def write_sequence(seq, output=None, format="long", use_translator=True):
"""
Write amino acid sequence in the desired format either to a stream
given or to STDOUT.
TODO: - add some flexibility to the output formats
"""
if output is None:
output = sys.stdout
if format == "long":
l = []
while seq:
s = seq.pop(0)
if use_translator:
s = omniTranslator(s.capitalize(), "3-letter-aminoacids")
l.append(s.upper())
if len(l) == 15:
output.write(" ".join(l) + "\n")
l = []
output.write(" ".join(l) + "\n")
elif format == "full":
l = []
while seq:
s = seq.pop(0)
if use_translator:
s = omniTranslator(s.capitalize(), "english")
l.append(s)
output.write(" ".join(l) + "\n")
else:
l = []
w = ""
while seq:
s = seq.pop(0)
if use_translator:
s = omniTranslator(s.capitalize(), "1-letter-aminoacids")
w += s.upper()
if len(w) == 10:
l.append(w)
w = ""
if len(l) == 6:
output.write(" ".join(l) + "\n")
l = []
if w:
l.append(w)
output.write(" ".join(l) + "\n")
def parse_sequence(args):
"""
Parse an amino acid sequence.
Arguments:
args -- a list of sequence items or a name of a file containing
them, e.g. 'GLU PRO GLU CYS' or 'EPEC GLK C EEK'
Returns:
sequence -- a list of 3-letter amino acid symbols
"""
loki.debug('parse_sequence < %s' % repr(args))
if isinstance(args, str) and os.path.isfile(args):
fname = args
elif len(args) == 1 and isinstance(args[0], str):
if os.path.isfile(args[0]):
fname = args[0]
else:
if args[0].count(' '):
args = args[0].split()
else:
args = args[0]
fname = None
else:
fname = None
if fname:
f = open(fname)
seq = f.read()
f.close()
loki.info("Read sequence from file '%s'." % fname)
args = seq.strip().split()
loki.debug('args=%s' % repr(args))
# sequence = []
# for aa in seq.strip().split():
# try:
# sequence.append(omniTranslator(aa.capitalize(), \
# '3-letter-aminoacids'))
# except KeyError:
# loki.warn("Discarding unknown aminoacid '%s'." % repr(aa))
# else:
# check whether all the sequence items are separated from each other
args = [x.capitalize() for x in args]
separated = True
for a in args:
if not (a in libLingua.dictionaryAmino1 or \
a in libLingua.dictionaryAmino3):
separated = False
loki.debug('separated=%s' % repr(separated))
sequence = []
if separated:
# append each item after converting it to a 3-letter symbol
for a in args:
try:
sequence.append(omniTranslator(a.capitalize(), \
'3-letter-aminoacids'))
except KeyError:
loki.warn("Discarding unknown aminoacid '%s'." % repr(a))
else:
# jam all symbols together (hope they are all 1-letter symbols)
aa = ''
for a in args:
aa += str(a)
aa = aa.replace(' ', '')
loki.debug('aa=%s' % repr(aa))
# append each item after converting it to a 3-letter symbol
for a in list(aa):
try:
sequence.append(omniTranslator(a, '3-letter-aminoacids'))
except KeyError:
loki.warn("Discarding unknown aminoacid '%s'." % repr(a))
loki.debug('parse_sequence > %s' % repr(sequence))
return sequence
def parse_sequence(args):
"""
Parse an amino acid sequence.
Arguments:
args -- a list of sequence items or a name of a file containing
them, e.g. 'GLU PRO GLU CYS' or 'EPEC GLK C EEK'
Returns:
sequence -- a list of 3-letter amino acid symbols
"""
loki.debug("parse_sequence < %s" % repr(args))
if isinstance(args, str) and os.path.isfile(args):
fname = args
elif len(args) == 1 and isinstance(args[0], str):
if os.path.isfile(args[0]):
fname = args[0]
else:
if args[0].count(" "):
args = args[0].split()
else:
args = args[0]
fname = None
else:
fname = None
if fname:
f = open(fname)
seq = f.read()
f.close()
loki.info("Read sequence from file '%s'." % fname)
args = seq.strip().split()
loki.debug("args=%s" % repr(args))
# sequence = []
# for aa in seq.strip().split():
# try:
# sequence.append(omniTranslator(aa.capitalize(), \
# '3-letter-aminoacids'))
# except KeyError:
# loki.warn("Discarding unknown aminoacid '%s'." % repr(aa))
# else:
# check whether all the sequence items are separated from each other
args = [x.capitalize() for x in args]
separated = True
for a in args:
if not (a in libLingua.dictionaryAmino1 or a in libLingua.dictionaryAmino3):
separated = False
loki.debug("separated=%s" % repr(separated))
sequence = []
if separated:
# append each item after converting it to a 3-letter symbol
for a in args:
try:
sequence.append(omniTranslator(a.capitalize(), "3-letter-aminoacids"))
except KeyError:
loki.warn("Discarding unknown aminoacid '%s'." % repr(a))
else:
# jam all symbols together (hope they are all 1-letter symbols)
aa = ""
for a in args:
aa += str(a)
aa = aa.replace(" ", "")
loki.debug("aa=%s" % repr(aa))
# append each item after converting it to a 3-letter symbol
for a in list(aa):
try:
sequence.append(omniTranslator(a, "3-letter-aminoacids"))
except KeyError:
loki.warn("Discarding unknown aminoacid '%s'." % repr(a))
loki.debug("parse_sequence > %s" % repr(sequence))
return sequence