biofiles 0.0.10__py3-none-any.whl → 0.0.12__py3-none-any.whl

biofiles/fai.py

@@ -0,0 +1,23 @@
+import sys
+from typing import Iterator
+
+from biofiles.common import Reader
+from biofiles.types.sequence import SequenceDescription
+
+
+class FAIReader(Reader):
+    def __iter__(self) -> Iterator[SequenceDescription]:
+        for line in self._input:
+            sequence_id, length_str, byte_offset_str, _, _ = line.rstrip("\n").split(
+                "\t"
+            )
+            yield SequenceDescription(
+                id=sequence_id, length=int(length_str), byte_offset=int(byte_offset_str)
+            )
+
+
+if __name__ == "__main__":
+    for path in sys.argv[1:]:
+        with FAIReader(path) as reader:
+            for seq_desc in reader:
+                print(seq_desc)

biofiles/types/alignment.py

@@ -1,7 +1,15 @@
 from dataclasses import dataclass
 
 
-__all__ = ["ReferenceSequence", "Alignment", "BAMTag"]
+__all__ = [
+    "Alignment",
+    "BAMFlag",
+    "BAMTag",
+    "CIGAR",
+    "CIGAROpKind",
+    "CIGAROperation",
+    "ReferenceSequence",
+]
 
 from enum import IntFlag
 

biofiles/types/sequence.py

@@ -9,3 +9,10 @@ class Sequence:
     id: str
     description: str
     sequence: str
+
+
+@dataclass(frozen=True)
+class SequenceDescription:
+    id: str
+    length: int
+    byte_offset: int

biofiles/utility/feature.py

@@ -183,7 +183,7 @@ class FeatureReader(Reader):
 
     def _finalize_other(self, draft: FeatureDraft, result: Features) -> Feature:
         parent_id = self._extract_parent_id(draft)
-        parent = result.by_id[parent_id] if parent_id is not None else None
+        parent = result.by_id.get(parent_id) if parent_id is not None else None
 
         return Feature(
             sequence_id=draft.sequence_id,

{biofiles-0.0.10.dist-info → biofiles-0.0.12.dist-info}/METADATA

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: biofiles
-Version: 0.0.10
+Version: 0.0.12
 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>
@@ -36,6 +36,7 @@ Classifier: Programming Language :: Python :: 3.12
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
+Dynamic: license-file
 
 # biofiles
 

{biofiles-0.0.10.dist-info → biofiles-0.0.12.dist-info}/RECORD

@@ -1,20 +1,21 @@
 biofiles/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biofiles/bam.py,sha256=w32LLOAuKWdGF7joTSrB4HYXCdfvvijZW44jizG36R8,6771
 biofiles/common.py,sha256=Yi0i85FpD2wR3vqL645LTUAE6TybGDxxZQsUmEGHqu4,1126
+biofiles/fai.py,sha256=gG2oDmaU7PIIYYBc8LiudaeKdo-6WIdwsMDIM7qi098,678
 biofiles/fasta.py,sha256=ctIt5I_fcZx-xQN921zpmlZS7e9_ICf-3_i6mTs5qbs,2135
 biofiles/gff.py,sha256=b3apOmJNoiy_qQHtyUSnNh0s999B6gyAODyjI7fN15g,6246
 biofiles/gtf.py,sha256=h_eFKnYWb8GQp-CX9EPZRodUba-bzQLGidGHOPUo4iM,2366
 biofiles/repeatmasker.py,sha256=txOYdw15ru88pUczsk0pDFzgGpplLu23CB8Ppz-MczY,3119
 biofiles/types/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-biofiles/types/alignment.py,sha256=5UvwKJ2psIpkkU5efGRHe8gYhMIoW35-RZ_Zoe5YDrY,1612
+biofiles/types/alignment.py,sha256=Kc0XteLyfj1gNJNLsUgzSKzAAoMobhkJyPFsovaU7dM,1696
 biofiles/types/feature.py,sha256=3Ar45WRgiaDSh5iQt24Emtk6_57G01q5nHJ1GNIJ19Y,1190
 biofiles/types/repeat.py,sha256=63SqzAwEGIDIGP9pxC85RUdwXbbSm0S5WNL3lSiWlmc,641
-biofiles/types/sequence.py,sha256=EOw_oKuMR0THpCYJqVE__27z7qrRqcdIPrRWTL4OFMw,152
+biofiles/types/sequence.py,sha256=XeJ3wgi8AwRaVYVKmf41y5mOmWQfdsS8ysaRLZWbNoQ,254
 biofiles/utility/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biofiles/utility/cli.py,sha256=bkUzmT5R4qdJ0YtA4LNU5JYpimD1HmZlHtoSaKzDsUc,4032
-biofiles/utility/feature.py,sha256=tUTn16xV1e0qpgkZ1ZwQ4LJJGil5mgQJBJ9s1yFDgiI,8068
-biofiles-0.0.10.dist-info/LICENSE,sha256=CbR8ssdFyViKj25JAlMjIt1_FbiZ1tAC5t-uwUbxqak,1070
-biofiles-0.0.10.dist-info/METADATA,sha256=jthXyKbpyvig9dgiQmUaIyDH8hWKX2zMyojyIxr5mjM,3034
-biofiles-0.0.10.dist-info/WHEEL,sha256=52BFRY2Up02UkjOa29eZOS2VxUrpPORXg1pkohGGUS8,91
-biofiles-0.0.10.dist-info/top_level.txt,sha256=laFaFv8hpkI4U-Pgs0yBaAJXN2_CJKl7jb-m3-tGfSc,9
-biofiles-0.0.10.dist-info/RECORD,,
+biofiles/utility/feature.py,sha256=5sKCbKrZndBuO-_DZBuaXJc_URKTY8NMToJ786lALZA,8072
+biofiles-0.0.12.dist-info/licenses/LICENSE,sha256=CbR8ssdFyViKj25JAlMjIt1_FbiZ1tAC5t-uwUbxqak,1070
+biofiles-0.0.12.dist-info/METADATA,sha256=8CRRV3Yr1Yp5APxIcRS-qv7EN1oCGcWjvjEXbi5A4hY,3056
+biofiles-0.0.12.dist-info/WHEEL,sha256=zaaOINJESkSfm_4HQVc5ssNzHCPXhJm0kEUakpsEHaU,91
+biofiles-0.0.12.dist-info/top_level.txt,sha256=laFaFv8hpkI4U-Pgs0yBaAJXN2_CJKl7jb-m3-tGfSc,9
+biofiles-0.0.12.dist-info/RECORD,,

{biofiles-0.0.10.dist-info → biofiles-0.0.12.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (76.0.0)
+Generator: setuptools (80.8.0)
 Root-Is-Purelib: true
 Tag: py3-none-any