def get_protein_sequence(self, seq_dict, frame, truncate=True):
"""
Returns the protein sequence for this ChromosomeInterval, in frame.
:param seq_dict: Dictionary-like object with DNA sequences.
:param frame: an integer between 0 and 2
:param truncate: Truncate to multiple of 3. Do this if you are on an non-terminal exon.
:return: A sequence string.
"""
seq = self.get_sequence(seq_dict)
if truncate:
return translate_sequence(seq[frame:len(seq) - len(seq) % 3])
else:
return translate_sequence(seq[frame:len(seq)])
def get_protein_sequence(self, seq_dict):
"""
Returns the translated protein sequence for this transcript in single
character space.
"""
cds = self.get_cds(seq_dict)
if len(cds) < 3:
return ''
return translate_sequence(self.get_cds(seq_dict).upper())
def get_protein_sequence(self, seq_dict):
"""
Returns the translated protein sequence for this transcript in single
character space.
"""
cds = self.get_cds(seq_dict)
if len(cds) < 3:
return ''
return translate_sequence(self.get_cds(seq_dict).upper())
def get_protein_sequence(self, seq_dict):
"""
Returns the translated protein sequence for this transcript in single character space.
"""
cds = self.get_cds(seq_dict, ignore_frameshift=True)
if len(cds) < 3:
return ""
try:
return translate_sequence(cds.upper())
except AssertionError:
raise RuntimeError('Failed to translate transcript {} with sequence {}'.format(self.name, cds))
def get_protein_sequence(self, seq_dict):
"""
Returns the translated protein sequence for this transcript in single character space.
"""
cds = self.get_cds(seq_dict, ignore_frameshift=True)
if len(cds) < 3:
return ""
try:
return translate_sequence(cds.upper())
except AssertionError:
raise RuntimeError(
'Failed to translate transcript {} with sequence {}'.format(
self.name, cds))