Remove --text flag from cat utility

Author: Donaim

micall/drivers/sample.py

@@ -435,7 +435,7 @@ def run_denovo(self, excluded_seeds):
         concatenate_files(inputs=[self.unstitched_contigs_fasta,
                                   self.merged_contigs_fasta],
                           output=self.combined_contigs_fasta,
-                          text=True, ignore_not_found=True)
+                          ignore_not_found=True)
 
         with open(self.combined_contigs_fasta, 'r') as combined_contigs_fasta, \
              open(self.stitched_contigs_fasta, 'w') as stitched_contigs_fasta:

micall/utils/cat.py

@@ -21,7 +21,6 @@
 
 def cat(inputs: Iterable[Path],
         output: Path,
-        text: bool,
         ignore_not_found: bool,
         ) -> int:
 
@@ -33,7 +32,6 @@ def cat(inputs: Iterable[Path],
         inputs (Paths): List of input file paths.
         output (Path): Path to the output file where the result
         will be saved.
-        text (bool): Whether to treat inputs as text.
         ignore_not_found (bool): Whether to treat non-existant inputs as empty.
     """
 
@@ -42,11 +40,7 @@ def cat(inputs: Iterable[Path],
             for file in inputs:
                 try:
                     with open(file) as f:
-                        if text:
-                            for line in f:
-                                out.write(line)
-                        else:
-                            shutil.copyfileobj(f, out)
+                        shutil.copyfileobj(f, out)
                 except FileNotFoundError:
                     if ignore_not_found:
                         continue
@@ -71,8 +65,6 @@ def main(argv: Sequence[str]) -> int:
     parser = argparse.ArgumentParser(
         description="Concatenate inputs and write to an output file.")
 
-    parser.add_argument('--text', action='store_true',
-                        help='Operate on text inputs.')
     parser.add_argument('--ignore-not-found', action='store_true',
                         help='Treat non-existant inputs as empty.')