def validate_secstruc(secstruc):
"""Checks vienna string format"""
if re.search("^[\(\)\.]*$", secstruc):
return secstruc
raise ParameterError(
"Bad parameter: '%s' must be a RNA secondary structure in dot-bracket format."
% str(secstruc))
def validate_resnum(resnum):
"""Checks residue number format"""
resnum = str(resnum)
if re.search("^\d+\w*$", resnum):
return resnum
raise ParameterError("Bad parameter: '%s' must be a residue number." %
str(resnum))
def validate_path(path, exist=True):
"""Checks path names."""
if exist:
if path != '' and not os.path.exists(path):
raise ParameterError(
"Bad parameter: '%s' must be a valid path name." % str(path))
return path
def validate_resi_list(resi_list, length=None):
"""Checks list of residues"""
if hasattr(resi_list, '__iter__'):
resi_list = [validate_resi(resi) for resi in resi_list]
if length == None or length == len(resi_list):
return resi_list
raise ParameterError("Bad parameter: '%s' must be a list of residues." %
str(resi_list))
def validate_seq(seq):
"""Checks sequence format"""
if isinstance(seq, Sequence):
return seq
elif type(seq) == str:
seq = Sequence(seq)
return seq
raise ParameterError("Bad parameter: '%s' must be a RNA sequence." %
str(seq))
def validate_alignment(ali):
"""Checks alignment string or object"""
if isinstance(ali, RNAAlignment):
return ali
elif isinstance(ali, str):
return read_alignment(ali)
raise ParameterError(
"Bad parameter: '%s' must be a pairwise Alignment (object or fasta string)."
% str(ali))
def validate_alphabet_list(alphabet_list, length=None):
"""Checks list of residue names"""
if hasattr(alphabet_list, '__iter__') or isinstance(alphabet_list, str):
alphabet_list = [validate_alphabet(alpha) for alpha in alphabet_list]
if length == None or length == len(alphabet_list):
return alphabet_list
raise ParameterError(
"Bad parameter: '%s' must be a list of residue names." %
str(alphabet_list))
def validate_filename(filename, exist=False):
"""Checks file names"""
if exist:
if not os.path.exists(filename):
raise ParameterError(
"Bad parameter: '%s' must be a valid file name." %
str(filename))
else:
path = os.path.dirname(filename)
validate_path(path)
return filename
def validate_alphabet(alpha):
"""Checks residue names."""
if str(alpha) in alphabet:
return alphabet[str(alpha)].long_abbrev
else:
try:
return alphabet.get_short_original(str(alpha)).long_abbrev
except AlphabetError:
pass
raise ParameterError("Bad parameter: '%s' must be a valid residue name." %
str(alpha))
def validate_fragment(frag):
"""Checks RnaModel object"""
if isinstance(frag, ModernaFragment) or isinstance(frag, LirHit):
return frag
raise ParameterError(
"Bad parameter: '%s' must be a ModernaFragment object." % str(frag))
def validate_model(model):
"""Checks RnaModel object"""
if isinstance(model, RnaModel):
return model
raise ParameterError("Bad parameter: '%s' must be a RnaModel object." %
str(model))
def validate_template(template):
"""Checks Template object"""
if isinstance(template, Template):
return template
raise ParameterError("Bad parameter: '%s' must be a Template object." %
str(template))
def validate_structure(struc):
"""Checks for ModernaStructure objects."""
if isinstance(struc, ModernaStructure):
return struc
raise ParameterError("Bad parameter: '%s' must be a structure object." %
str(struc))
def validate_resi(resi):
"""Checks RNAResidue"""
if isinstance(resi, RNAResidue):
return resi
raise ParameterError("Bad parameter: '%s' must be a ModeRNAResidue." %
str(resi))
def validate_frag_candidate_list(fc_list):
if isinstance(fc_list, FragmentCandidates):
return fc_list
raise ParameterError(
"Bad parameter: '%s' must be a list of fragment candidates." %
str(fc_list))
