From 49ef3dfbcc5a4ceef69f5fe83cf2aa137d63829d Mon Sep 17 00:00:00 2001 From: Jeremy Arbesfeld Date: Mon, 9 Dec 2024 09:09:11 -0500 Subject: [PATCH] Fix docstrings --- src/cool_seq_tool/mappers/exon_genomic_coords.py | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/src/cool_seq_tool/mappers/exon_genomic_coords.py b/src/cool_seq_tool/mappers/exon_genomic_coords.py index 2717012..683df69 100644 --- a/src/cool_seq_tool/mappers/exon_genomic_coords.py +++ b/src/cool_seq_tool/mappers/exon_genomic_coords.py @@ -461,7 +461,7 @@ async def genomic_to_tx_segment( :param gene: A valid, case-sensitive HGNC symbol. Must be given if no ``transcript`` value is provided. :param coordinate_type: Coordinate type for ``seg_start_genomic`` and - ``seg_end_genomic`` + ``seg_end_genomic``. Expects inter-residue coordinates by default :return: Genomic data (inter-residue coordinates) """ errors = [] @@ -747,7 +747,6 @@ async def _genomic_to_tx_segment( errors. :param genomic_pos: Genomic position where the transcript segment starts or ends - (inter-residue based) :param chromosome: Chromosome. Must give chromosome without a prefix (i.e. ``1`` or ``X``). If not provided, must provide ``genomic_ac``. If position maps to both GRCh37 and GRCh38, GRCh38 assembly will be used. @@ -769,7 +768,7 @@ async def _genomic_to_tx_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 coordinate_type: Coordinate type for ``seg_start_genomic`` and - ``seg_end_genomic`` + ``seg_end_genomic``. Expects inter-residue coordinates by default :return: Data for a transcript segment boundary (inter-residue coordinates) """ params = {key: None for key in GenomicTxSeg.model_fields} @@ -1180,7 +1179,7 @@ def _use_alt_start_i(is_seg_start: bool, strand: Strand) -> bool: :return ``True`` if alt_start_i should be used, ``False`` if alt_end_i should be used """ - return bool( + return ( is_seg_start and strand == Strand.POSITIVE or not is_seg_start @@ -1249,7 +1248,8 @@ def _get_exon_offset( """Compute offset from exon start or end index :param genomic_pos: The supplied genomic position. This can represent, for - example, a fusion junction breakpoint + example, a fusion junction breakpoint. This position is represented using + inter-residue coordinates :param exon_boundary: The genomic position for the exon boundary that the offset is being computed against :paran strand: The transcribed strand