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refactor: rename is_start kwarg in private methods to is_seg_start #359

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merged 4 commits into from
Aug 23, 2024
Merged

refactor: rename is_start kwarg in private methods to is_seg_start #359

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7d1e26b
refactor!: rename `ExonCoord` to `_ExonCoord` to indicate internal use
korikuzma Aug 20, 2024
1539ccc
refactor: reorder classes and methods in exon_genomic_coords module
korikuzma Aug 21, 2024
b9d80fc
refactor: rename `is_start` kwarg in private methods to `is_seg_start`
korikuzma Aug 21, 2024
302c058
Merge branch 'main' into rename-is-start
korikuzma Aug 23, 2024
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42 changes: 22 additions & 20 deletions src/cool_seq_tool/mappers/exon_genomic_coords.py
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Original file line number Diff line number Diff line change
Expand Up @@ -479,7 +479,7 @@ async def genomic_to_tx_segment(
transcript=transcript,
gene=gene,
get_nearest_transcript_junction=get_nearest_transcript_junction,
is_start=True,
is_seg_start=True,
)
if start_tx_seg_data.errors:
return _return_service_errors(start_tx_seg_data.errors)
Expand All @@ -499,7 +499,7 @@ async def genomic_to_tx_segment(
transcript=transcript,
gene=gene,
get_nearest_transcript_junction=get_nearest_transcript_junction,
is_start=False,
is_seg_start=False,
)
if end_tx_seg_data.errors:
return _return_service_errors(end_tx_seg_data.errors)
Expand Down Expand Up @@ -689,7 +689,7 @@ def _get_tx_segment(
genomic_loc, err_msg = self._get_vrs_seq_loc(
genomic_ac,
seg_genomic_pos,
is_start=is_seg_start,
is_seg_start=is_seg_start,
strand=strand,
)
if err_msg:
Expand All @@ -702,14 +702,14 @@ def _get_tx_segment(
), None

def _get_vrs_seq_loc(
self, genomic_ac: str, genomic_pos: int, is_start: bool, strand: Strand
self, genomic_ac: str, genomic_pos: int, is_seg_start: bool, strand: Strand
) -> tuple[SequenceLocation | None, str | None]:
"""Create VRS Sequence Location for genomic position where transcript segment
occurs

:param genomic_ac: RefSeq genomic accession
:param genomic_pos: Genomic position where the transcript segment occurs
:param is_start: ``True`` if ``genomic_pos`` is where the transcript segment
:param is_seg_start: ``True`` if ``genomic_pos`` is where the transcript segment
starts. ``False`` if ``genomic_pos`` is where the transcript segment ends.
:param strand: Strand
:return: Tuple containing VRS location (if successful) and error message (if
Expand All @@ -721,7 +721,9 @@ def _get_vrs_seq_loc(
if err_msg:
return None, err_msg

use_start = strand == Strand.POSITIVE if is_start else strand != Strand.POSITIVE
use_start = (
strand == Strand.POSITIVE if is_seg_start else strand != Strand.POSITIVE
)

return SequenceLocation(
sequenceReference=SequenceReference(
Expand All @@ -739,7 +741,7 @@ async def _genomic_to_tx_segment(
transcript: str | None = None,
gene: str | None = None,
get_nearest_transcript_junction: bool = False,
is_start: bool = True,
is_seg_start: bool = True,
) -> GenomicTxSeg:
"""Given genomic data, generate a boundary for a transcript segment.

Expand All @@ -766,7 +768,7 @@ async def _genomic_to_tx_segment(
following the breakpoint for the 3' end. For the negative strand, adjacent
is defined as the exon following the breakpoint for the 5' end and the exon
preceding the breakpoint for the 3' end.
:param is_start: ``True`` if ``genomic_pos`` is where the transcript segment starts.
:param is_seg_start: ``True`` if ``genomic_pos`` is where the transcript segment starts.
``False`` if ``genomic_pos`` is where the transcript segment ends.
:return: Data for a transcript segment boundary (inter-residue coordinates)
"""
Expand Down Expand Up @@ -847,24 +849,24 @@ async def _genomic_to_tx_segment(
exon_num = self._get_adjacent_exon(
tx_exons_genomic_coords=tx_exons,
strand=strand,
start=genomic_pos if is_start else None,
end=genomic_pos if not is_start else None,
start=genomic_pos if is_seg_start else None,
end=genomic_pos if not is_seg_start else None,
)

offset = self._get_exon_offset(
start_i=tx_exons[exon_num].alt_start_i,
end_i=tx_exons[exon_num].alt_end_i,
strand=strand,
use_start_i=strand == Strand.POSITIVE
if is_start
if is_seg_start
else strand != Strand.POSITIVE,
is_in_exon=False,
start=genomic_pos if is_start else None,
end=genomic_pos if not is_start else None,
start=genomic_pos if is_seg_start else None,
end=genomic_pos if not is_seg_start else None,
)

genomic_location, err_msg = self._get_vrs_seq_loc(
genomic_ac, genomic_pos, is_start, strand
genomic_ac, genomic_pos, is_seg_start, strand
)
if err_msg:
return GenomicTxSeg(errors=[err_msg])
Expand Down Expand Up @@ -932,7 +934,7 @@ async def _genomic_to_tx_segment(
)

return await self._get_tx_seg_genomic_metadata(
genomic_ac, genomic_pos, is_start, gene, tx_ac=transcript
genomic_ac, genomic_pos, is_seg_start, gene, tx_ac=transcript
)

async def _get_grch38_ac_pos(
Expand Down Expand Up @@ -1021,7 +1023,7 @@ async def _get_tx_seg_genomic_metadata(
self,
genomic_ac: str,
genomic_pos: int,
is_start: bool,
is_seg_start: bool,
gene: str,
tx_ac: str | None,
) -> GenomicTxSeg:
Expand All @@ -1034,7 +1036,7 @@ async def _get_tx_seg_genomic_metadata(

:param genomic_ac: Genomic RefSeq accession
:param genomic_pos: Genomic position where the transcript segment occurs
:param is_start: Whether or not ``genomic_pos`` represents the start position.
:param is_seg_start: Whether or not ``genomic_pos`` represents the start position.
:param gene: HGNC gene symbol
:param tx_ac: Transcript RefSeq accession. If not provided, will use MANE
transcript
Expand Down Expand Up @@ -1092,12 +1094,12 @@ async def _get_tx_seg_genomic_metadata(
strand=Strand(tx_exon_aln_data.alt_strand),
use_start_i=False, # This doesn't impact anything since we're on the exon
is_in_exon=True,
start=genomic_pos if is_start else None,
end=genomic_pos if not is_start else None,
start=genomic_pos if is_seg_start else None,
end=genomic_pos if not is_seg_start else None,
)

genomic_location, err_msg = self._get_vrs_seq_loc(
genomic_ac, genomic_pos, is_start, tx_exon_aln_data.alt_strand
genomic_ac, genomic_pos, is_seg_start, tx_exon_aln_data.alt_strand
)
if err_msg:
return GenomicTxSeg(errors=[err_msg])
Expand Down
6 changes: 3 additions & 3 deletions tests/mappers/test_exon_genomic_coords.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1020,20 +1020,20 @@ async def test_genomic_to_transcript(test_egc_mapper, tpm3_exon1, tpm3_exon8):
154170399,
genomic_ac="NC_000001.11",
transcript="NM_152263.3",
is_start=False,
is_seg_start=False,
)
genomic_tx_seg_checks(resp, tpm3_exon8)

resp = await test_egc_mapper._genomic_to_tx_segment(
154170399,
chromosome="1",
transcript="NM_152263.3",
is_start=False,
is_seg_start=False,
)
genomic_tx_seg_checks(resp, tpm3_exon8)

resp = await test_egc_mapper._genomic_to_tx_segment(
154170399, chromosome="1", transcript="NM_152263.3", is_start=False
154170399, chromosome="1", transcript="NM_152263.3", is_seg_start=False
)
genomic_tx_seg_checks(resp, tpm3_exon8)

Expand Down