pybiolib 1.2.102.dev1__tar.gz → 1.2.106.dev1__tar.gz

{pybiolib-1.2.102.dev1 → pybiolib-1.2.106.dev1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pybiolib
-Version: 1.2.102.dev1
+Version: 1.2.106.dev1
 Summary: BioLib Python Client
 Home-page: https://github.com/biolib
 License: MIT

{pybiolib-1.2.102.dev1 → pybiolib-1.2.106.dev1}/biolib/utils/seq_util.py

@@ -1,5 +1,5 @@
 import re
-from io import BufferedIOBase, TextIOWrapper
+from io import BufferedIOBase, TextIOBase
 
 from biolib.typing_utils import Dict, List, Optional, Union, Iterator
 
@@ -59,7 +59,7 @@ class SeqUtil:
             for line in file_handle:
                 yield line.decode('utf-8')
 
-        def line_generator_from_text_io_wrapper(file_handle: TextIOWrapper) -> Iterator[str]:
+        def line_generator_from_text_io_base(file_handle: TextIOBase) -> Iterator[str]:
             for line in file_handle:
                 yield line
 
@@ -71,10 +71,12 @@ class SeqUtil:
 
         file_handle = None
         if isinstance(input_file, str):
-            file_handle = open(input_file, "r")
-            line_iterator = line_generator_from_text_io_wrapper(file_handle)
+            file_handle = open(input_file, "rb")
+            line_iterator = line_generator_from_buffered_io_base(file_handle)
         elif isinstance(input_file, BufferedIOBase):
             line_iterator = line_generator_from_buffered_io_base(input_file)
+        elif isinstance(input_file, TextIOBase):
+            line_iterator = line_generator_from_text_io_base(input_file)
         else:
             raise ValueError('input_file must be a file name (str) or a BufferedIOBase object')
 
@@ -84,6 +86,8 @@ class SeqUtil:
         try:
             for line_number, line in enumerate(line_iterator):
                 line = line.strip()
+                if not line:
+                    continue # skip empty lines
                 if line.startswith('>'):
                     if header is not None:
                         yield from process_and_yield_record(header, sequence_lines)

{pybiolib-1.2.102.dev1 → pybiolib-1.2.106.dev1}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pybiolib"
-version = "1.2.102.dev1"
+version = "1.2.106.dev1"
 description = "BioLib Python Client"
 readme = "PYPI_README.md"
 license = "MIT"