refactor: update read_sequencer.py

readsequencer/read_sequencer.py

@@ -23,8 +23,8 @@ class ReadSequencer:
 
     def __init__(
         self,
-        fasta: str = None,
-        output: str = None,
+        fasta: str,
+        output: str,
         read_length: int = 150,
         chunk_size: int = 10000,
     ) -> None:
@@ -35,7 +35,7 @@ class ReadSequencer:
         self.chunk_size = chunk_size
         self.random = False
         self.bases = ("A", "T", "C", "G")
-        self.n_sequences = None
+        self.n_sequences: int
 
     def get_n_sequences(self) -> None:
         """Detect number of sequences present in set fasta file.
@@ -135,11 +135,18 @@ class ReadSequencer:
                     range(self.n_sequences), self.chunk_size
                 )
                 for i, batch in enumerate(batch_generator):
-                    filename = self.output.replace(".fasta", "") + f"_chunk_{i}.fasta" % (i + 1)
-                    with open(filename, "w", encoding="utf-8") as output_handle:
-                        for j, k in enumerate(batch):
+                    filename = (
+                        self.output.replace(".fasta", "") +
+                        f"_chunk_{i}.fasta" % (i + 1)
+                    )
+                    with open(
+                        filename, "w", encoding="utf-8"
+                    ) as output_handle:
+                        for j, _ in enumerate(batch):
                             record = SeqRecord(
-                                self.generate_random_sequence(self.read_length),
+                                self.generate_random_sequence(
+                                    self.read_length
+                                ),
                                 id="random_seq: " + str(j + 1),
                             )
                             SeqIO.write(record, output_handle, "fasta")
@@ -153,12 +160,16 @@ class ReadSequencer:
                         SeqIO.write(record, output_handle, "fasta")
 
             else:
-                record_iter = SeqIO.parse(open(self.fasta, encoding="utf-8"), "fasta")
-                for i, batch in enumerate(
-                    self.batch_iterator(record_iter, self.chunk_size)
-                ):
-                    filename = self.output.replace(".fasta", "") + "_chunk_%i.fasta" % (i + 1)
-                    for j, record in enumerate(batch):
-                        batch[j].seq = self.resize_sequence(record)
-                    with open(filename, "w") as handle:
-                        SeqIO.write(batch, handle, "fasta")
+                with open(self.fasta, encoding="utf-8") as file:
+                    record_iter = SeqIO.parse(file, "fasta")
+                    for i, batch in enumerate(
+                        self.batch_iterator(record_iter, self.chunk_size)
+                    ):
+                        filename = (
+                            self.output.replace(".fasta", "") +
+                            f"_chunk_{i}.fasta" % (i + 1)
+                        )
+                        for j, record in enumerate(batch):
+                            batch[j].seq = self.resize_sequence(record)
+                        with open(filename, "w", encoding="utf-8") as handle:
+                            SeqIO.write(batch, handle, "fasta")

setup.py

@@ -14,8 +14,8 @@ setup(
     license='MIT',
     author='Clara Serger, Michael Sandholzer and Christoph Harmel',
     author_email='christoph.harmel@unibas.ch',
-    description='Simulates sequencing with a specified read length from \
-        sequences specified by a FASTA file.',
+    description='Simulates sequencing with a specified read length from'
+                'sequences specified by a FASTA file.',
     packages=find_packages(),
     install_requires=INSTALL_REQUIRED,
     entry_points={'console_scripts': ['readsequencer=readsequencer.cli:main']}