def __init__(self, seq_list, temp=50, nupack_home=None, rna1999=False):
'''
:param seq_list: Input sequence(s).
:type seq_list: coral.DNA, coral.RNA, or list of
either.
:param rna1999: Use RNA 1999 settings.
:type rna1999: bool
:param temp: Temperature in C.
:type temp: float
:param nupack_home: NUPACK home dir. The script attempts to find the
NUPACKHOME environment variable if this isn't set.
:type nupack_home: str
:returns: Nupack instance.
:raises: ValueError if NUPACKHOME environment variable is not defined
and nupack_home is undefined.
ValueError if sequences are not all the same type (e.g. don't
mix RNA and DNA).
Exception if using rna1999 with a Tm other than 37C.
'''
# Set up nupack environment variable
if nupack_home is None:
if 'NUPACKHOME' in environ:
nupack_home = environ['NUPACKHOME']
else:
msg1 = 'Must have NUPACKHOME environment variable set or '
msg2 = 'set nupack_home argument.'
raise ValueError(msg1 + msg2)
self._nupack_home = nupack_home
# If input isn't list, make it one
if not isinstance(seq_list, list):
self._seq_list = [seq_list]
else:
self._seq_list = seq_list
# Figure out material based on input and ensure it's consistent
self._material = sequence_type(self._seq_list[0])
if not all([sequence_type(seq) == self._material for seq in
self._seq_list]):
raise ValueError('Sequence inputs were of mixed types.')
# Convert seq object(s) to string(s)
self._seq_list = [str(seq) for seq in self._seq_list]
# Shared temperature input
self._temp = temp
# Handle rna1999 setting
if self._material == 'rna' and rna1999:
self._material = 'rna1999'
if self._temp != 37:
raise Exception('To use rna1999 settings, temp must be 37.')
# Create temp dir
self._tempdir = mkdtemp()
# Track whether complexes has been run to avoid redundant computation
self._complexes_run = False
self._complexes_file = None
def __init__(self, seq_list, temp=50, nupack_home=None, rna1999=False):
'''
:param seq_list: Input sequence(s).
:type seq_list: coral.DNA, coral.RNA, or list of
either.
:param rna1999: Use RNA 1999 settings.
:type rna1999: bool
:param temp: Temperature in C.
:type temp: float
:param nupack_home: NUPACK home dir. The script attempts to find the
NUPACKHOME environment variable if this isn't set.
:type nupack_home: str
:returns: Nupack instance.
:raises: ValueError if NUPACKHOME environment variable is not defined
and nupack_home is undefined.
ValueError if sequences are not all the same type (e.g. don't
mix RNA and DNA).
Exception if using rna1999 with a Tm other than 37C.
'''
# Set up nupack environment variable
if nupack_home is None:
if 'NUPACKHOME' in environ:
nupack_home = environ['NUPACKHOME']
else:
msg1 = 'Must have NUPACKHOME environment variable set or '
msg2 = 'set nupack_home argument.'
raise ValueError(msg1 + msg2)
self._nupack_home = nupack_home
# If input isn't list, make it one
if type(seq_list) != list:
self._seq_list = [seq_list]
else:
self._seq_list = seq_list
# Figure out material based on input and ensure it's consistent
self._material = sequence_type(self._seq_list[0])
if not all(
[sequence_type(seq) == self._material for seq in self._seq_list]):
raise ValueError('Sequence inputs were of mixed types.')
# Convert seq object(s) to string(s)
self._seq_list = [str(seq) for seq in self._seq_list]
# Shared temperature input
self._temp = temp
# Handle rna1999 setting
if self._material == 'rna' and rna1999:
self._material = 'rna1999'
if self._temp != 37:
raise Exception('To use rna1999 settings, temp must be 37.')
# Create temp dir
self._tempdir = mkdtemp()
# Track whether complexes has been run to avoid redundant computation
self._complexes_run = False
self._complexes_file = None
def __init__(self, seq_list, dotbrackets=None, constraint_structures=None):
'''
:param seq: DNA or RNA sequences to evaluate.
:type seq: list of coral.DNA, coral.RNA, or str
:param dotbrackets: Dot bracket formatted structures of given seuqneces
:type dotbrackets: list of str
:returns: coral.analysis.Vienna instance.
'''
# If input isn't list, make it one
if not isinstance(seq_list, list):
self._seq_list = [seq_list]
else:
self._seq_list = seq_list
# Figure out material based on input and ensure it's consistent
self._material = sequence_type(self._seq_list[0])
if not all([sequence_type(seq) == self._material for seq in
self._seq_list]):
raise ValueError('Sequence inputs were of mixed types.')
# Convert seq object(s) to string(s)
self._seq_list = [str(seq) for seq in self._seq_list]
self._tempdir = ''
if dotbrackets is None:
self.dotbrackets = []
else:
self.dotbrackets = dotbrackets
if constraint_structures is None:
self.constraint_structures = []
else:
self.constraint_structures = constraint_structures
