biofiles 0.0.10__tar.gz → 0.0.12__tar.gz

{biofiles-0.0.10 → biofiles-0.0.12}/PKG-INFO

@@ -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-0.0.12/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-0.0.10 → biofiles-0.0.12}/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-0.0.10 → biofiles-0.0.12}/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-0.0.10 → biofiles-0.0.12}/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 → biofiles-0.0.12}/biofiles.egg-info/PKG-INFO

@@ -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 → biofiles-0.0.12}/biofiles.egg-info/SOURCES.txt

@@ -4,6 +4,7 @@ pyproject.toml
 biofiles/__init__.py
 biofiles/bam.py
 biofiles/common.py
+biofiles/fai.py
 biofiles/fasta.py
 biofiles/gff.py
 biofiles/gtf.py

{biofiles-0.0.10 → biofiles-0.0.12}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "biofiles"
-version = "0.0.10"
+version = "0.0.12"
 authors = [
   { name="Tigran Saluev", email="tigran@saluev.com" },
 ]