biofiles 0.0.4__py3-none-any.whl → 0.0.5__py3-none-any.whl

biofiles/gff.py

@@ -5,7 +5,7 @@ from pathlib import Path
 from typing import Iterator, cast, TextIO
 
 from biofiles.common import Strand, Reader, Writer
-from biofiles.types.feature import Feature, Gene, Exon
+from biofiles.types.feature import Feature, Gene, Exon, ThreePrimeUTR
 
 __all__ = ["GFFReader", "GFF3Writer"]
 
@@ -173,11 +173,13 @@ class GFFReader(Reader):
         yield from result.features
 
     def _finalize_draft(self, draft: _FeatureDraft, result: _Features) -> Feature:
-        match draft.type_:
+        match draft.type_.lower():
             case "gene":
                 feature = self._finalize_gene(draft, result)
             case "exon":
                 feature = self._finalize_exon(draft, result)
+            case "three_prime_utr":
+                feature = self._finalize_three_prime_utr(draft, result)
             case _:
                 feature = self._finalize_other(draft, result)
         if feature.parent:
@@ -206,6 +208,19 @@ class GFFReader(Reader):
         object.__setattr__(gene, "exons", gene.exons + (exon,))
         return exon
 
+    def _finalize_three_prime_utr(
+        self, draft: _FeatureDraft, result: _Features
+    ) -> Feature:
+        feature = self._finalize_other(draft, result)
+
+        gene = feature.parent
+        while gene and not isinstance(gene, Gene):
+            gene = gene.parent
+
+        if gene is None:
+            return feature
+        return ThreePrimeUTR(**feature.__dict__, gene=gene)
+
     def _finalize_other(self, draft: _FeatureDraft, result: _Features) -> Feature:
         parent_id = draft.attributes.get("Parent", None)
         parent = result.by_id[parent_id] if parent_id is not None else None

biofiles/types/feature.py

@@ -43,3 +43,9 @@ class Gene(Feature):
 class Exon(Feature):
     gene: Gene
     # TODO transcript, mRNA
+
+
+@dataclass(frozen=True)
+class ThreePrimeUTR(Feature):
+    gene: Gene
+    # TODO transcript

{biofiles-0.0.4.dist-info → biofiles-0.0.5.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: biofiles
-Version: 0.0.4
+Version: 0.0.5
 Summary: Pure-Python, zero-dependency collection of bioinformatics-related file readers and writers
 Author-email: Tigran Saluev <tigran@saluev.com>
 Maintainer-email: Tigran Saluev <tigran@saluev.com>

{biofiles-0.0.4.dist-info → biofiles-0.0.5.dist-info}/RECORD

@@ -1,14 +1,14 @@
 biofiles/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biofiles/common.py,sha256=Yi0i85FpD2wR3vqL645LTUAE6TybGDxxZQsUmEGHqu4,1126
 biofiles/fasta.py,sha256=ctIt5I_fcZx-xQN921zpmlZS7e9_ICf-3_i6mTs5qbs,2135
-biofiles/gff.py,sha256=Bag0Z1xNR8l4IDEGct6OU2gCjmRldKRrhKcw8gNjbMY,10629
+biofiles/gff.py,sha256=lSS7XxS4rpCesCc9FTG87E8p4eJYgtzN9lcz9Y5WNDk,11148
 biofiles/repeatmasker.py,sha256=DqD1z1hUfCP4-qnfjF-oMF-ZpW_6XhOf_nzA8VHhQbw,3079
 biofiles/types/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-biofiles/types/feature.py,sha256=c9m_DU_EaUIWG6-xsiPxQIiGkfDs96nm5ls2T5SMeuA,826
+biofiles/types/feature.py,sha256=eMBrL0OQGo0MRjM7Sqmo-AKxMb0rJb1Cwc1ygp5BfPY,919
 biofiles/types/repeat.py,sha256=63SqzAwEGIDIGP9pxC85RUdwXbbSm0S5WNL3lSiWlmc,641
 biofiles/types/sequence.py,sha256=EOw_oKuMR0THpCYJqVE__27z7qrRqcdIPrRWTL4OFMw,152
-biofiles-0.0.4.dist-info/LICENSE,sha256=CbR8ssdFyViKj25JAlMjIt1_FbiZ1tAC5t-uwUbxqak,1070
-biofiles-0.0.4.dist-info/METADATA,sha256=X4kN2G9g266dSlVtZ7RPuh2PUXtdu_0W41rPL_-hPzE,3033
-biofiles-0.0.4.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
-biofiles-0.0.4.dist-info/top_level.txt,sha256=laFaFv8hpkI4U-Pgs0yBaAJXN2_CJKl7jb-m3-tGfSc,9
-biofiles-0.0.4.dist-info/RECORD,,
+biofiles-0.0.5.dist-info/LICENSE,sha256=CbR8ssdFyViKj25JAlMjIt1_FbiZ1tAC5t-uwUbxqak,1070
+biofiles-0.0.5.dist-info/METADATA,sha256=cSInsFiXUGdvIK11QTD24SkhW1lWmd7DyHvd5hjE8PY,3033
+biofiles-0.0.5.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
+biofiles-0.0.5.dist-info/top_level.txt,sha256=laFaFv8hpkI4U-Pgs0yBaAJXN2_CJKl7jb-m3-tGfSc,9
+biofiles-0.0.5.dist-info/RECORD,,