def parse_external_result(self, _file):
result = {"Seq":{}, self.name:{}}
count = 0
is_new_seq = 0
for l in _file:
l = l.strip()
if not len(l):
continue
#print l
if not is_new_seq % 4 and is_new_seq:
#print "New seq starts", l
count +=1
is_new_seq = 0
elif l[0] == "-":
#print "in counter", l
is_new_seq += 1
elif l[0].isdigit():
pos,aa,_,s,_ = l.split()
pos = int(pos) - 1
seq_id = "seq_%i"%count
result["Seq"][(seq_id, pos)] = aa
result[self.name][(seq_id, pos)] = float(s)
df_result = CleavageSitePredictionResult.from_dict(result)
df_result.index = pandas.MultiIndex.from_tuples([tuple((i,j)) for i,j in df_result.index],
names=['ID','Pos'])
return df_result
def predict(self, _aa_seq, command=None, options=None, **kwargs):
"""
Overwrites ACleavageSitePrediction.predict
:param list(Peptide/Protein)/Peptide/Protein _aa_seq: A list of or a single Peptide or Protein object
:param str command: The path to a alternative binary (can be used if binary is not globally executable)
:param str options: A string of additional options directly past to the external tool.
:return: CleavageSitePredictionResult - A CleavageSitePredictionResult object
"""
if not self.is_in_path() and "path" not in kwargs:
raise RuntimeError("{name} {version} could not be found in PATH".format(name=self.name,
version=self.version))
external_version = self.get_external_version(path=command)
if self.version != external_version and external_version is not None:
raise RuntimeError("Internal version {internal_version} does "
"not match external version {external_version}".format(internal_version=self.version,
external_version=external_version))
if isinstance(_aa_seq, Peptide) or isinstance(_aa_seq, Protein):
pep_seqs = {str(_aa_seq): _aa_seq}
else:
if any((not isinstance(p, Peptide)) and (not isinstance(p, Protein)) for p in _aa_seq):
raise ValueError("Input is not of type Protein or Peptide")
pep_seqs = {str(p): p for p in _aa_seq}
tmp_out = NamedTemporaryFile(delete=False)
tmp_file = NamedTemporaryFile(delete=False)
self.prepare_input(pep_seqs.iterkeys(), tmp_file)
tmp_file.close()
#allowe customary executable specification
if command is not None:
exe = self.command.split()[0]
_command = self.command.replace(exe, command)
else:
_command = self.command
try:
stdo = None
stde = None
cmd = _command.format(peptides=tmp_file.name, options="" if options is None else options, out=tmp_out.name)
p = subprocess.Popen(cmd, shell=True, stdin=subprocess.PIPE, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
stdo, stde = p.communicate()
stdr = p.returncode
if stdr > 0:
raise RuntimeError("Unsuccessful execution of " + cmd + " (EXIT!=0) with error: " + stde)
except Exception as e:
raise RuntimeError(e)
result = self.parse_external_result(tmp_out)
df_result = CleavageSitePredictionResult.from_dict(result)
df_result.index = pandas.MultiIndex.from_tuples([tuple((i,j)) for i, j in df_result.index],
names=['ID', 'Pos'])
os.remove(tmp_file.name)
tmp_out.close()
os.remove(tmp_out.name)
return df_result
def predict(self, aa_seq, length=None, **kwargs):
"""
Returns predictions for given peptides an alleles. If no alleles are given, predictions for all available models
are made.
:param list(Peptide)/Peptide peptides: A single Peptide or a list of Peptides
:param kwargs: optional parameter (not used yet)
:return: Returns a AResult object with the prediction results
"""
def __load_model(length):
model = "%s_%i"%(self.name, length)
return getattr(__import__("Fred2.Data.pssms."+self.name+".mat."+model, fromlist=[model]),
model)
if isinstance(aa_seq, Peptide) or isinstance(aa_seq, Protein):
pep_seqs = {str(aa_seq):aa_seq}
else:
if any((not isinstance(p, Peptide)) and (not isinstance(p, Protein)) for p in aa_seq):
raise ValueError("Input is not of type Protein or Peptide")
pep_seqs = {str(p):p for p in aa_seq}
length = min(self.supportedLength) if length is None else length
if length not in self.supportedLength:
raise ValueError("Length %i is not supported by %s"%(length, self.name))
#group peptides by length and
result = {"Seq":{},self.name:{}}
try:
pssm = __load_model(length)
except ImportError:
raise KeyError("No model found for %s with length %i"%(self.name, length))
diff = length - self.cleavagePos
for j,seq in enumerate(pep_seqs.iterkeys()):
seq_id = "seq_%i"%j
p = pep_seqs[seq]
if isinstance(p, Protein):
if p.transcript_id:
seq_id = p.transcript_id
else:
for t in p.proteins.iterkeys():
if t:
seq_id = t
break
#dynamicaly import prediction PSSMS for alleles and predict
if len(seq) < length:
warnings.warn("Sequence length of %i is to small for specified window of %i"%(len(seq),length), RuntimeWarning)
continue
for i in xrange(len(seq)):
if i < (length-1):
result["Seq"][(seq_id, i)] = seq[i]
result[self.name][(seq_id, i)] = 0.0
else:
result[self.name][(seq_id, i)] = 0.0
result["Seq"][(seq_id, i)] = seq[i]
score = sum(pssm.get(i,{}).get(aa,0) for i,aa in enumerate(seq[i-(length-1):(i+1)]))+pssm.get(-1,{}).get("con",0)
result[self.name][(seq_id, i-diff)] = score
if not result["Seq"]:
raise ValueError("No predictions could be made for the given input.")
df_result = CleavageSitePredictionResult.from_dict(result)
df_result.index = pandas.MultiIndex.from_tuples([tuple((i,j)) for i,j in df_result.index],
names=['ID','Pos'])
return df_result
def predict(self, aa_seq, command=None, options=None, **kwargs):
"""
Overwrites ACleavageSitePrediction.predict
:param aa_seq: A list of or a single :class:`~Fred2.Core.Peptide.Peptide` or :class:`~Fred2.Core.Protein.Protein` object
:type aa_seq: list(:class:`~Fred2.Core.Peptide.Peptide`/:class:`~Fred2.Core.Protein.Protein`) or :class:`~Fred2.Core.Peptide.Peptide`/:class:`~Fred2.Core.Protein.Protein`
:param str command: The path to a alternative binary (can be used if binary is not globally executable)
:param str options: A string of additional options directly past to the external tool
:return: A :class:`~Fred2.Core.CleavageSitePredictionResult` object
:rtype: :class:`~Fred2.Core.CleavageSitePredictionResult`
"""
if not self.is_in_path() and "path" not in kwargs and command is None:
raise RuntimeError(
"{name} {version} could not be found in PATH".format(
name=self.name, version=self.version))
external_version = self.get_external_version(path=command)
if self.version != external_version and external_version is not None:
raise RuntimeError(
"Internal version {internal_version} does "
"not match external version {external_version}".format(
internal_version=self.version,
external_version=external_version))
if isinstance(aa_seq, Peptide) or isinstance(aa_seq, Protein):
pep_seqs = {str(aa_seq): aa_seq}
else:
pep_seqs = {}
for p in aa_seq:
if not isinstance(p, Peptide) and not isinstance(p, Protein):
raise ValueError("Input is not of type Protein or Peptide")
pep_seqs[str(p)] = p
chunksize = len(pep_seqs)
if 'chunks' in kwargs:
chunksize = kwargs['chunks']
result = {}
peps = list(pep_seqs.values())
for i in range(0, len(peps), chunksize):
tmp_out = NamedTemporaryFile(delete=False)
tmp_file = NamedTemporaryFile(delete=False)
self.prepare_input(peps[i:i + chunksize], tmp_file)
tmp_file.close()
#allowe customary executable specification
if command is not None:
exe = self.command.split()[0]
_command = self.command.replace(exe, command)
else:
_command = self.command
try:
stdo = None
stde = None
cmd = _command.format(
input=tmp_file.name,
options="" if options is None else options,
out=tmp_out.name)
p = subprocess.Popen(cmd,
shell=True,
stdin=subprocess.PIPE,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
stdo, stde = p.communicate()
stdr = p.returncode
if stdr > 0:
raise RuntimeError("Unsuccessful execution of " + cmd +
" (EXIT!=0) with error: " + stde)
except Exception as e:
raise RuntimeError(e)
result.update(self.parse_external_result(tmp_out))
os.remove(tmp_file.name)
tmp_out.close()
os.remove(tmp_out.name)
df_result = CleavageSitePredictionResult.from_dict(result)
df_result.index = pandas.MultiIndex.from_tuples(
[tuple((i, j)) for i, j in df_result.index], names=['ID', 'Pos'])
return df_result
def predict(self, aa_seq, length=None, **kwargs):
"""
Returns predictions for given peptides.
:param aa_seq: A single :class:`~Fred2.Core.Peptide.Peptide` or `~Fred2.Core.Protein.Protein` or a list of
:class:`~Fred2.Core.Peptide` or :class:`~Fred2.Core.Protein.Protein`
:type aa_seq: list(:class:`~Fred2.Core.Peptide.Peptide` or :class:`~Fred2.Core.Protein.Protein`)
or :class:`~Fred2.Core.Peptide`/:class:`~Fred2.Core.Protein.Protein`
:param int length: The peptide length of the cleavage site model. If None the default value is used.
:return: Returns a :class:`~Fred2.Core.Result.CleavageSitePredictionResult` object
:rtype: :class:`~Fred2.Core.Result.CleavageSitePredictionResult`
"""
def __load_model(length):
model = "%s_%i" % (self.name, length)
return getattr(
__import__("Fred2.Data.pssms." + self.name + ".mat." + model,
fromlist=[model]), model)
if isinstance(aa_seq, Peptide) or isinstance(aa_seq, Protein):
pep_seqs = {str(aa_seq): aa_seq}
else:
pep_seqs = {}
for p in aa_seq:
if not isinstance(p, Peptide) and not isinstance(p, Protein):
raise ValueError("Input is not of type Protein or Peptide")
pep_seqs[str(p)] = p
length = min(self.supportedLength) if length is None else length
if length not in self.supportedLength:
raise ValueError("Length %i is not supported by %s" %
(length, self.name))
#group peptides by length and
result = {"Seq": {}, self.name: {}}
try:
pssm = __load_model(length)
except ImportError:
raise KeyError("No model found for %s with length %i" %
(self.name, length))
diff = length - self.cleavagePos
for j, seq in enumerate(pep_seqs.keys()):
seq_id = "seq_%i" % j
p = pep_seqs[seq]
if isinstance(p, Protein):
if p.transcript_id:
seq_id = p.transcript_id
else:
for t in p.proteins.keys():
if t:
seq_id = t
break
#dynamicaly import prediction PSSMS for alleles and predict
if len(seq) < length:
warnings.warn(
"Sequence length of %i is to small for specified window of %i"
% (len(seq), length), RuntimeWarning)
continue
for i in range(len(seq)):
if i < (length - 1):
result["Seq"][(seq_id, i)] = seq[i]
result[self.name][(seq_id, i)] = 0.0
else:
result[self.name][(seq_id, i)] = 0.0
result["Seq"][(seq_id, i)] = seq[i]
score = sum(
pssm.get(i, {}).get(aa, 0)
for i, aa in enumerate(seq[i - (length - 1):(
i + 1)])) + pssm.get(-1, {}).get("con", 0)
result[self.name][(seq_id, i - diff)] = score
if not result["Seq"]:
raise ValueError(
"No predictions could be made for the given input.")
df_result = CleavageSitePredictionResult.from_dict(result)
df_result.index = pandas.MultiIndex.from_tuples(
[tuple((i, j)) for i, j in df_result.index], names=['ID', 'Pos'])
return df_result
def predict(self, aa_seq, command=None, options=None, **kwargs):
"""
Overwrites ACleavageSitePrediction.predict
:param aa_seq: A list of or a single :class:`~Fred2.Core.Peptide.Peptide` or :class:`~Fred2.Core.Protein.Protein` object
:type aa_seq: list(:class:`~Fred2.Core.Peptide.Peptide`/:class:`~Fred2.Core.Protein.Protein`) or :class:`~Fred2.Core.Peptide.Peptide`/:class:`~Fred2.Core.Protein.Protein`
:param str command: The path to a alternative binary (can be used if binary is not globally executable)
:param str options: A string of additional options directly past to the external tool
:return: A :class:`~Fred2.Core.CleavageSitePredictionResult` object
:rtype: :class:`~Fred2.Core.CleavageSitePredictionResult`
"""
if not self.is_in_path() and "path" not in kwargs:
raise RuntimeError("{name} {version} could not be found in PATH".format(name=self.name,
version=self.version))
external_version = self.get_external_version(path=command)
if self.version != external_version and external_version is not None:
raise RuntimeError("Internal version {internal_version} does "
"not match external version {external_version}".format(internal_version=self.version,
external_version=external_version))
if isinstance(aa_seq, Peptide) or isinstance(aa_seq, Protein):
pep_seqs = {str(aa_seq): aa_seq}
else:
pep_seqs = {}
for p in aa_seq:
if not isinstance(p, Peptide) and not isinstance(p, Protein):
raise ValueError("Input is not of type Protein or Peptide")
pep_seqs[str(p)] = p
chunksize = len(pep_seqs)
if 'chunks' in kwargs:
chunksize = kwargs['chunks']
result = {}
peps = list(pep_seqs.values())
for i in xrange(0, len(peps), chunksize):
tmp_out = NamedTemporaryFile(delete=False)
tmp_file = NamedTemporaryFile(delete=False)
self.prepare_input(peps[i:i+chunksize], tmp_file)
tmp_file.close()
#allowe customary executable specification
if command is not None:
exe = self.command.split()[0]
_command = self.command.replace(exe, command)
else:
_command = self.command
try:
stdo = None
stde = None
cmd = _command.format(input=tmp_file.name, options="" if options is None else options, out=tmp_out.name)
p = subprocess.Popen(cmd, shell=True, stdin=subprocess.PIPE, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
stdo, stde = p.communicate()
stdr = p.returncode
if stdr > 0:
raise RuntimeError("Unsuccessful execution of " + cmd + " (EXIT!=0) with error: " + stde)
except Exception as e:
raise RuntimeError(e)
result.update(self.parse_external_result(tmp_out))
os.remove(tmp_file.name)
tmp_out.close()
os.remove(tmp_out.name)
df_result = CleavageSitePredictionResult.from_dict(result)
df_result.index = pandas.MultiIndex.from_tuples([tuple((i,j)) for i, j in df_result.index],
names=['ID', 'Pos'])
return df_result
def predict(self, aa_seq, command=None, options=None, **kwargs):
"""
Overwrites ACleavageSitePrediction.predict
:param aa_seq: A list of or a single :class:`~Fred2.Core.Peptide.Peptide` or :class:`~Fred2.Core.Protein.Protein` object
:type aa_seq: list(:class:`~Fred2.Core.Peptide.Peptide`/:class:`~Fred2.Core.Protein.Protein`) or :class:`~Fred2.Core.Peptide.Peptide`/:class:`~Fred2.Core.Protein.Protein`
:param str command: The path to a alternative binary (can be used if binary is not globally executable)
:param str options: A string of additional options directly past to the external tool
:return: A :class:`~Fred2.Core.CleavageSitePredictionResult` object
:rtype: :class:`~Fred2.Core.CleavageSitePredictionResult`
"""
if not self.is_in_path() and "path" not in kwargs:
raise RuntimeError(
"{name} {version} could not be found in PATH".format(
name=self.name, version=self.version))
external_version = self.get_external_version(path=command)
if self.version != external_version and external_version is not None:
raise RuntimeError(
"Internal version {internal_version} does "
"not match external version {external_version}".format(
internal_version=self.version,
external_version=external_version))
#Since NetChop 3.1 cuts identifiers to 10-digits we use
#An integer hashing to generate unique ids for
#With is we can predict 99999999999 protein sequences simultaniously
#After reaching the limit one could revers the counting in the negative
#direction
if isinstance(aa_seq, Peptide) or isinstance(aa_seq, Protein):
pep_seqs = {str(aa_seq): aa_seq}
else:
pep_seqs = {}
for i, p in enumerate(aa_seq):
if not isinstance(p, Peptide) and not isinstance(p, Protein):
raise ValueError("Input is not of type Protein or Peptide")
if i < 99999999999:
pep_seqs[i] = p
else:
pep_seqs[i - 99999999999] = p
tmp_out = NamedTemporaryFile(delete=False)
tmp_file = NamedTemporaryFile(delete=False)
self.prepare_input(pep_seqs, tmp_file)
tmp_file.close()
#allowe customary executable specification
if command is not None:
exe = self.command.split()[0]
_command = self.command.replace(exe, command)
else:
_command = self.command
try:
stdo = None
stde = None
cmd = _command.format(input=tmp_file.name,
options="" if options is None else options,
out=tmp_out.name)
p = subprocess.Popen(cmd,
shell=True,
stdin=subprocess.PIPE,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
stdo, stde = p.communicate()
stdr = p.returncode
if stdr > 0:
raise RuntimeError("Unsuccessful execution of " + cmd +
" (EXIT!=0) with error: " + stde)
except Exception as e:
raise RuntimeError(e)
result = self.parse_external_result(tmp_out, pep_seqs)
df_result = CleavageSitePredictionResult.from_dict(result)
df_result.index = pandas.MultiIndex.from_tuples(
[tuple((i, j)) for i, j in df_result.index], names=['ID', 'Pos'])
os.remove(tmp_file.name)
tmp_out.close()
os.remove(tmp_out.name)
return df_result