biofiles 0.1.1__py3-none-any.whl → 0.1.3__py3-none-any.whl

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Files changed (8) hide show
  1. biofiles/dialects/gencode.py +2 -2
  2. biofiles/dialects/genomic_base.py +3 -2
  3. biofiles/dialects/refseq.py +2 -2
  4. {biofiles-0.1.1.dist-info → biofiles-0.1.3.dist-info}/METADATA +1 -1
  5. {biofiles-0.1.1.dist-info → biofiles-0.1.3.dist-info}/RECORD +8 -8
  6. {biofiles-0.1.1.dist-info → biofiles-0.1.3.dist-info}/WHEEL +0 -0
  7. {biofiles-0.1.1.dist-info → biofiles-0.1.3.dist-info}/licenses/LICENSE +0 -0
  8. {biofiles-0.1.1.dist-info → biofiles-0.1.3.dist-info}/top_level.txt +0 -0
biofiles/dialects/gencode.py CHANGED
@@ -144,7 +144,7 @@ stop_codon_exon, _ = relation(source=("transcript_id", "exon_number"), one_to_on
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  class Gene(BaseGene, type="gene"):
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  id: str = id_field(source="gene_id")
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- type: GeneType = field(source="gene_type")
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+ biotype: GeneType = field(source="gene_type")
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  name: str = field(source="gene_name")
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  transcripts: list["Transcript"] = gene_transcripts
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  tags: list[str] = field(source="tag", default_factory=list)
@@ -152,7 +152,7 @@ class Gene(BaseGene, type="gene"):
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  class Transcript(BaseTranscript, type="transcript"):
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  id: str = id_field(source="transcript_id")
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- type: TranscriptType = field(source="transcript_type")
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+ biotype: TranscriptType = field(source="transcript_type")
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  name: str = field(source="transcript_name")
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  gene: Gene = transcript_gene
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  exons: list["Exon"] = transcript_exons
biofiles/dialects/genomic_base.py CHANGED
@@ -2,12 +2,13 @@ from biofiles.types.feature import Feature
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  class Gene(Feature):
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- type: str
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+ biotype: str
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+ name: str
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  transcripts: list["Transcript"]
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  class Transcript(Feature):
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- type: str
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+ biotype: str
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  gene: Gene
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  exons: list["Exon"]
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biofiles/dialects/refseq.py CHANGED
@@ -90,7 +90,7 @@ stop_codon_exon, _ = relation(source=("transcript_id", "exon_number"), one_to_on
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  class Gene(BaseGene, type="gene"):
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  id: str = id_field(source="gene_id")
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- type: GeneType = field(source="gene_biotype")
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+ biotype: GeneType = field(source="gene_biotype")
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  name: str = field(source="gene")
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  synonyms: list[str] = field(source="gene_synonym", default_factory=list)
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  transcripts: list["Transcript"] = gene_transcripts
@@ -98,7 +98,7 @@ class Gene(BaseGene, type="gene"):
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  class Transcript(BaseTranscript, type="transcript"):
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  id: str = id_field(source="transcript_id")
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- type: TranscriptType = field(source="transcript_biotype")
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+ biotype: TranscriptType = field(source="transcript_biotype")
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  product: str | None = field(source="product", default=None)
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  gene: Gene = transcript_gene
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  exons: list["Exon"] = transcript_exons
{biofiles-0.1.1.dist-info → biofiles-0.1.3.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: biofiles
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- Version: 0.1.1
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+ Version: 0.1.3
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  Summary: Pure-Python, zero-dependency collection of bioinformatics-related file readers and writers
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  Author-email: Tigran Saluev <tigran@saluev.com>
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  Maintainer-email: Tigran Saluev <tigran@saluev.com>
{biofiles-0.1.1.dist-info → biofiles-0.1.3.dist-info}/RECORD RENAMED
@@ -8,9 +8,9 @@ biofiles/gtf.py,sha256=wCtHzLTCqR-oAGPtiRDJ4GvyS_Z5FzmLLzw8lgTj5Ig,3490
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  biofiles/repeatmasker.py,sha256=7KObXELCHQ6oBkO8yK6Znrs6MX8sfVuxNSmOMe0Ogfk,3289
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  biofiles/dialects/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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  biofiles/dialects/detector.py,sha256=OP42NhQf3s609fmDaRRFEMawgf0VMZdeAfkbK6IL4yM,2461
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- biofiles/dialects/gencode.py,sha256=4XyHZfrvxDm64bWnEYyatmkKtFgdgZynCXpiCGQ8OnY,7724
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- biofiles/dialects/genomic_base.py,sha256=JOVmVHj3DNboZK79v4Ofj5qNRWpABZrUDdMntFZkx4U,356
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- biofiles/dialects/refseq.py,sha256=UYjDb5S98hjhfD1tPAIY796E0ditsZAvc-u5qSKfvOk,4211
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+ biofiles/dialects/gencode.py,sha256=oxTKmcipalgdhy_eNhCqRd5Rdchz8Pn1SXlQHlg6YuM,7730
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+ biofiles/dialects/genomic_base.py,sha256=QHLzCLGckYmEEWc8qSYmr6u7LJW3LHLoo6op2x-c9zI,376
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+ biofiles/dialects/refseq.py,sha256=ZjTpm-AOLs2jQRU9G4V11uiAAtrJop1OF-HyDIr-IrI,4217
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  biofiles/dialects/stringtie.py,sha256=kuQ6IWRo7c4xkNjN-4jjYy3_dRUPorMaffYvDYvQDD8,834
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  biofiles/types/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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  biofiles/types/alignment.py,sha256=Kc0XteLyfj1gNJNLsUgzSKzAAoMobhkJyPFsovaU7dM,1696
@@ -20,8 +20,8 @@ biofiles/types/sequence.py,sha256=XeJ3wgi8AwRaVYVKmf41y5mOmWQfdsS8ysaRLZWbNoQ,25
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  biofiles/utility/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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  biofiles/utility/cli.py,sha256=i2kYpPFnpTYdbd_6T-U9-egitKhDGQVDbw5gme4Kelg,4074
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  biofiles/utility/feature.py,sha256=bHUOfYir_Dfk_DEBrlO1GXvkJKDRkpj2YJfSl4w698s,7931
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- biofiles-0.1.1.dist-info/licenses/LICENSE,sha256=CbR8ssdFyViKj25JAlMjIt1_FbiZ1tAC5t-uwUbxqak,1070
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- biofiles-0.1.1.dist-info/METADATA,sha256=8maXLM85bmqcLfjZ-f3H_LolE62pd1J7YWERqc__Nt0,3361
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- biofiles-0.1.1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
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- biofiles-0.1.1.dist-info/top_level.txt,sha256=laFaFv8hpkI4U-Pgs0yBaAJXN2_CJKl7jb-m3-tGfSc,9
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- biofiles-0.1.1.dist-info/RECORD,,
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+ biofiles-0.1.3.dist-info/licenses/LICENSE,sha256=CbR8ssdFyViKj25JAlMjIt1_FbiZ1tAC5t-uwUbxqak,1070
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+ biofiles-0.1.3.dist-info/METADATA,sha256=FAJV7lyuzMD1u4_gj6QtUAp01ijotHiulKzddNMxLNk,3361
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+ biofiles-0.1.3.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
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+ biofiles-0.1.3.dist-info/top_level.txt,sha256=laFaFv8hpkI4U-Pgs0yBaAJXN2_CJKl7jb-m3-tGfSc,9
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+ biofiles-0.1.3.dist-info/RECORD,,