biofiles 0.0.10__py3-none-any.whl → 0.0.11__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/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.dist-info → biofiles-0.0.11.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: biofiles
-Version: 0.0.10
+Version: 0.0.11
 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-0.0.10.dist-info → biofiles-0.0.11.dist-info}/RECORD

@@ -1,6 +1,7 @@
 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
@@ -9,12 +10,12 @@ biofiles/types/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biofiles/types/alignment.py,sha256=5UvwKJ2psIpkkU5efGRHe8gYhMIoW35-RZ_Zoe5YDrY,1612
 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-0.0.11.dist-info/LICENSE,sha256=CbR8ssdFyViKj25JAlMjIt1_FbiZ1tAC5t-uwUbxqak,1070
+biofiles-0.0.11.dist-info/METADATA,sha256=LLFvSGArV0Iuse_720ylHhMBLhMB6HKVfZXYjdkNrEg,3034
+biofiles-0.0.11.dist-info/WHEEL,sha256=52BFRY2Up02UkjOa29eZOS2VxUrpPORXg1pkohGGUS8,91
+biofiles-0.0.11.dist-info/top_level.txt,sha256=laFaFv8hpkI4U-Pgs0yBaAJXN2_CJKl7jb-m3-tGfSc,9
+biofiles-0.0.11.dist-info/RECORD,,