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build: update CST version and pin ga4gh.vrs version (#216)
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@jarbesfeld
jarbesfeld authored Jan 9, 2025
1 parent 4a5e12d commit 69c1654
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Showing 2 changed files with 20 additions and 20 deletions.
4 changes: 2 additions & 2 deletions pyproject.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -27,10 +27,10 @@ license = {file = "LICENSE"}
dependencies = [
"pydantic ==2.*",
"polars ~= 1.0",
"ga4gh.vrs ~=2.0.0a10",
"ga4gh.vrs ==2.0.0a10",
"biocommons.seqrepo",
"gene-normalizer ==0.4.0",
"cool-seq-tool ~=0.8.0",
"cool-seq-tool ~=0.10.0",
]
dynamic=["version"]

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36 changes: 18 additions & 18 deletions src/fusor/translator.py
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Original file line number Diff line number Diff line change
Expand Up @@ -215,15 +215,15 @@ async def from_jaffa(
genomic_ac=self._get_genomic_ac(chrom1, rb),
seg_end_genomic=base1,
gene=gene_5prime,
get_nearest_transcript_junction=True,
starting_assembly=rb,
)

tr_3prime = await self.fusor.transcript_segment_element(
tx_to_genomic_coords=False,
genomic_ac=self._get_genomic_ac(chrom2, rb),
seg_start_genomic=base2,
gene=gene_3prime,
get_nearest_transcript_junction=True,
starting_assembly=rb,
)

if rearrangement:
Expand Down Expand Up @@ -275,15 +275,15 @@ async def from_star_fusion(
genomic_ac=self._get_genomic_ac(five_prime[0], rb),
seg_end_genomic=int(five_prime[1]),
gene=gene_5prime,
get_nearest_transcript_junction=True,
starting_assembly=rb,
)

tr_3prime = await self.fusor.transcript_segment_element(
tx_to_genomic_coords=False,
genomic_ac=self._get_genomic_ac(three_prime[0], rb),
seg_start_genomic=int(three_prime[1]),
gene=gene_3prime,
get_nearest_transcript_junction=True,
starting_assembly=rb,
)

ce = self._get_causative_event(five_prime[0], three_prime[0], ",".join(annots))
Expand Down Expand Up @@ -332,15 +332,15 @@ async def from_fusion_catcher(
genomic_ac=self._get_genomic_ac(five_prime[0], rb),
seg_end_genomic=int(five_prime[1]),
gene=gene_5prime_element.gene.label,
get_nearest_transcript_junction=True,
starting_assembly=rb,
)

tr_3prime = await self.fusor.transcript_segment_element(
tx_to_genomic_coords=False,
genomic_ac=self._get_genomic_ac(three_prime[0], rb),
seg_start_genomic=int(three_prime[1]),
gene=gene_3prime_element.gene.label,
get_nearest_transcript_junction=True,
starting_assembly=rb,
)

ce = self._get_causative_event(five_prime[0], three_prime[0], predicted_effect)
Expand Down Expand Up @@ -372,7 +372,7 @@ async def from_fusion_map(
),
seg_end_genomic=int(fmap_row.get_column("Position1").item()),
gene=gene_5prime,
get_nearest_transcript_junction=True,
starting_assembly=rb,
)

tr_3prime = await self.fusor.transcript_segment_element(
Expand All @@ -382,7 +382,7 @@ async def from_fusion_map(
),
seg_start_genomic=int(fmap_row.get_column("Position2").item()),
gene=gene_3prime,
get_nearest_transcript_junction=True,
starting_assembly=rb,
)

# Combine columns to create fusion annotation string"
Expand Down Expand Up @@ -467,7 +467,7 @@ async def from_arriba(
seg_start_genomic=int(breakpoint1[1]) if gene1_seg_start else None,
seg_end_genomic=int(breakpoint1[1]) if not gene1_seg_start else None,
gene=gene_5prime,
get_nearest_transcript_junction=True,
starting_assembly=rb,
)

tr_3prime = await self.fusor.transcript_segment_element(
Expand All @@ -476,7 +476,7 @@ async def from_arriba(
seg_start_genomic=int(breakpoint2[1]) if gene2_seg_start else None,
seg_end_genomic=int(breakpoint2[1]) if not gene2_seg_start else None,
gene=gene_3prime,
get_nearest_transcript_junction=True,
starting_assembly=rb,
)

ce = (
Expand Down Expand Up @@ -550,15 +550,15 @@ async def from_cicero(
genomic_ac=self._get_genomic_ac(chr_5prime, rb),
seg_end_genomic=pos_5prime,
gene=gene_5prime,
get_nearest_transcript_junction=True,
starting_assembly=rb,
)

tr_3prime = await self.fusor.transcript_segment_element(
tx_to_genomic_coords=False,
genomic_ac=self._get_genomic_ac(chr_3prime, rb),
seg_start_genomic=pos_3prime,
gene=gene_3prime,
get_nearest_transcript_junction=True,
starting_assembly=rb,
)

if event_type == "read_through":
Expand Down Expand Up @@ -603,15 +603,15 @@ async def from_mapsplice(
genomic_ac=self._get_genomic_ac(mapsplice_row[0].split("~")[0], rb),
seg_end_genomic=int(mapsplice_row[1]),
gene=gene_5prime,
get_nearest_transcript_junction=True,
starting_assembly=rb,
)

tr_3prime = await self.fusor.transcript_segment_element(
tx_to_genomic_coords=False,
genomic_ac=self._get_genomic_ac(mapsplice_row[0].split("~")[1], rb),
seg_start_genomic=int(mapsplice_row[2]),
gene=gene_3prime,
get_nearest_transcript_junction=True,
starting_assembly=rb,
)

ce = self._get_causative_event(
Expand Down Expand Up @@ -653,15 +653,15 @@ async def from_enfusion(
genomic_ac=self._get_genomic_ac(chr_5prime, rb),
seg_end_genomic=break_5prime,
gene=gene_5prime,
get_nearest_transcript_junction=True,
starting_assembly=rb,
)

tr_3prime = await self.fusor.transcript_segment_element(
tx_to_genomic_coords=False,
genomic_ac=self._get_genomic_ac(chr_3prime, rb),
seg_start_genomic=break_3prime,
gene=gene_3prime,
get_nearest_transcript_junction=True,
starting_assembly=rb,
)

ce = self._get_causative_event(
Expand Down Expand Up @@ -710,15 +710,15 @@ async def from_genie(
genomic_ac=self._get_genomic_ac(site1_chrom, rb),
seg_end_genomic=site1_pos,
gene=gene_5prime,
get_nearest_transcript_junction=True,
starting_assembly=rb,
)

tr_3prime = await self.fusor.transcript_segment_element(
tx_to_genomic_coords=False,
genomic_ac=self._get_genomic_ac(site2_chrom, rb),
seg_start_genomic=site2_pos,
gene=gene_3prime,
get_nearest_transcript_junction=True,
starting_assembly=rb,
)

ce = self._get_causative_event(
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