def chunk_relative_interval_to_cds(self, chr_start: int, chr_end: int, chr_strand: Strand) -> Location:
"""Converts a contiguous interval on the chunk-relative sequence to a relative location within the CDS."""
if not self.is_coding:
raise NoncodingTranscriptError("No CDS positions on non-coding transcript")
return self.cds.chunk_relative_location.parent_to_relative_location(
SingleInterval(chr_start, chr_end, chr_strand, parent=self.cds.chunk_relative_location.parent)
)
def get_protein_sequence(
self,
truncate_at_in_frame_stop: Optional[bool] = False,
translation_table: Optional[TranslationTable] = TranslationTable.DEFAULT,
) -> Sequence:
"""Return the translation of this transcript, if possible."""
if not self.is_coding:
raise NoncodingTranscriptError("No translation on non-coding transcript")
return self.cds.translate(
truncate_at_in_frame_stop=truncate_at_in_frame_stop, translation_table=translation_table
)
def get_3p_interval(self) -> Location:
"""Returns the 3' UTR as a location, if it exists.
WARNING: If this is a chunk-relative transcript, the result of this function will also be chunk-relative.
"""
if not self.is_coding:
raise NoncodingTranscriptError("No 3' UTR on a non-coding transcript")
# handle the edge case where the CDS is full length
if self.cds.chunk_relative_location == self.chunk_relative_location:
return EmptyLocation()
cds_inclusive_end_on_transcript = self.cds_pos_to_transcript(len(self.cds.chunk_relative_location) - 1)
return self.chunk_relative_location.relative_interval_to_parent_location(
cds_inclusive_end_on_transcript + 1, len(self._location), Strand.PLUS
)
def get_cds_sequence(self) -> Sequence:
"""Returns the in-frame CDS sequence (always multiple of 3)."""
if not self.is_coding:
raise NoncodingTranscriptError("No CDS sequence on non-coding transcript")
return self.cds.extract_sequence()
def transcript_pos_to_cds(self, pos: int) -> int:
"""Converts a relative position along this transcript to a relative position along the CDS."""
if not self.is_coding:
raise NoncodingTranscriptError("No CDS positions on non-coding transcript")
chr_pos = self.transcript_pos_to_sequence(pos)
return self.sequence_pos_to_cds(chr_pos)
def cds_interval_to_chunk_relative(self, rel_start: int, rel_end: int, rel_strand: Strand) -> Location:
"""Converts a contiguous interval relative to the CDS to a spliced location on the chunk-relative sequence."""
if not self.is_coding:
raise NoncodingTranscriptError("No CDS positions on non-coding transcript")
return self.cds.chunk_relative_location.relative_interval_to_parent_location(rel_start, rel_end, rel_strand)
def chunk_relative_pos_to_cds(self, pos: int) -> int:
"""Converts chunk-relative sequence position to relative position along the CDS."""
if not self.is_coding:
raise NoncodingTranscriptError("No CDS positions on non-coding transcript")
return self.cds.chunk_relative_location.parent_to_relative_pos(pos)
def chunk_relative_cds_blocks(self) -> List[Location]:
"""Wrapper for blocks function that reports blocks in chunk-relative coordinates"""
if self.is_coding:
return self.cds.chunk_relative_blocks
else:
raise NoncodingTranscriptError("No relative CDS blocks for non-coding transcript")
def cds_pos_to_chunk_relative(self, pos: int) -> int:
"""Converts a relative position along the CDS to chunk-relative sequence coordinate."""
if not self.is_coding:
raise NoncodingTranscriptError("No CDS positions on non-coding transcript")
return self.cds.chunk_relative_location.relative_to_parent_pos(pos)
def chunk_relative_cds_end(self) -> int:
if self.is_coding:
return self.cds_chunk_relative_location.end
else:
raise NoncodingTranscriptError("No CDS end for non-coding transcript")
def cds_blocks(self) -> Iterable[SingleInterval]:
"""Wrapper for blocks function that reports blocks in chromosome coordinates"""
if self.is_coding:
yield from self.cds.blocks
else:
raise NoncodingTranscriptError("No CDS blocks for non-coding transcript")
def chunk_relative_cds_start(self) -> int:
if self.is_coding:
return self.cds_chunk_relative_location.start
else:
raise NoncodingTranscriptError("No CDS start for non-coding transcript")
def cds_end(self) -> int:
if self.is_coding:
return self.cds.end
else:
raise NoncodingTranscriptError("No CDS end for non-coding transcript")
def cds_start(self) -> int:
if self.is_coding:
return self.cds.start
else:
raise NoncodingTranscriptError("No CDS start for non-coding transcript")
def has_in_frame_stop(self) -> bool:
if not self.is_coding:
raise NoncodingTranscriptError("Cannot have frameshifts on non-coding transcripts")
return self.cds.has_in_frame_stop
def cds_chunk_relative_location(self) -> Location:
"""Returns the Location of the CDS in *chunk relative coordinates*"""
if not self.is_coding:
raise NoncodingTranscriptError("No location on a non-coding transcript")
return self.cds.chunk_relative_location