biofiles 0.0.2__py3-none-any.whl → 0.0.4__py3-none-any.whl

biofiles/gff.py

@@ -4,10 +4,10 @@ from dataclasses import dataclass, field
 from pathlib import Path
 from typing import Iterator, cast, TextIO
 
-from biofiles.common import Strand, Reader
+from biofiles.common import Strand, Reader, Writer
 from biofiles.types.feature import Feature, Gene, Exon
 
-__all__ = ["GFFReader"]
+__all__ = ["GFFReader", "GFF3Writer"]
 
 
 @dataclass
@@ -261,6 +261,27 @@ class GFFReader(Reader):
         }
 
 
+class GFF3Writer(Writer):
+    def __init__(self, output: TextIO | Path | str) -> None:
+        super().__init__(output)
+        self._output.write(f"{_VERSION_PREFIX}3\n")
+
+    def write(self, feature: Feature) -> None:
+        fields = (
+            feature.sequence_id,
+            feature.source,
+            feature.type_,
+            str(feature.start_original),
+            str(feature.end_original),
+            str(feature.score) if feature.score is not None else ".",
+            str(feature.strand) if feature.strand is not None else ".",
+            str(feature.phase) if feature.phase is not None else ".",
+            ";".join(f"{k}={v}" for k, v in feature.attributes.items()),
+        )
+        self._output.write("\t".join(fields))
+        self._output.write("\n")
+
+
 _VERSION_PREFIX = "##gff-version "
 
 

{biofiles-0.0.2.dist-info → biofiles-0.0.4.dist-info}/METADATA

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: biofiles
-Version: 0.0.2
+Version: 0.0.4
 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-0.0.2.dist-info → biofiles-0.0.4.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=8pDiMgKAemIubv7qwOi8Qi6KEXCJI98XJobRSlAeXAE,9824
+biofiles/gff.py,sha256=Bag0Z1xNR8l4IDEGct6OU2gCjmRldKRrhKcw8gNjbMY,10629
 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/repeat.py,sha256=63SqzAwEGIDIGP9pxC85RUdwXbbSm0S5WNL3lSiWlmc,641
 biofiles/types/sequence.py,sha256=EOw_oKuMR0THpCYJqVE__27z7qrRqcdIPrRWTL4OFMw,152
-biofiles-0.0.2.dist-info/LICENSE,sha256=CbR8ssdFyViKj25JAlMjIt1_FbiZ1tAC5t-uwUbxqak,1070
-biofiles-0.0.2.dist-info/METADATA,sha256=eU82_wI02DtQOFeGE44s5HZeGQYutXXwa7TtjnNQxzg,3033
-biofiles-0.0.2.dist-info/WHEEL,sha256=PZUExdf71Ui_so67QXpySuHtCi3-J3wvF4ORK6k_S8U,91
-biofiles-0.0.2.dist-info/top_level.txt,sha256=laFaFv8hpkI4U-Pgs0yBaAJXN2_CJKl7jb-m3-tGfSc,9
-biofiles-0.0.2.dist-info/RECORD,,
+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-0.0.2.dist-info → biofiles-0.0.4.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.6.0)
+Generator: setuptools (75.8.0)
 Root-Is-Purelib: true
 Tag: py3-none-any