Format code with ruff

src/ngs_test_utils/testcase/__init__.py

@@ -1,4 +1,5 @@
 """Test case."""
+
 import os
 import tempfile
 import unittest

src/ngs_test_utils/testcase/bam.py

@@ -5,6 +5,7 @@
 [2] http://pysam.readthedocs.io/en/stable/usage.html#creating-bam-cram-sam-files-from-scratch
 
 """
+
 import os
 import random
 
@@ -72,8 +73,7 @@ def make_bam_segment(
         tags=None,
         **kwargs,
     ):
-        """
-        Return pysam.AlignedSegment object.
+        """Return pysam.AlignedSegment object.
 
         Each pysam.AlignedSegment element has 11 mandatory tab-separated
         fields (qname, flag, rname, pos, mapq, cigar, rnext, pnext,
@@ -87,7 +87,7 @@ def make_bam_segment(
         segment = pysam.AlignedSegment()
 
         if qname is None:
-            qname = "read-{}".format(random.randrange(1000, 9999))
+            qname = f"read-{random.randrange(1000, 9999)}"
         segment.query_name = qname
 
         segment.flag = flag or self.get_flag_value(**kwargs)
@@ -100,13 +100,17 @@ def make_bam_segment(
         segment.next_reference_start = pnext
         segment.template_length = tlen
 
-        length = sum([length for (operation, length) in segment.cigartuples if operation in [0, 1, 4, 7, 8]])
+        length = sum(
+            [length for (operation, length) in segment.cigartuples if operation in [0, 1, 4, 7, 8]]
+        )
         if seq is None:
             seq = FastaTestCaseMixin.make_fasta_sequence(size=length, include_n=False)
         segment.query_sequence = seq
 
         if qual is None:
-            qual = pysam.qualitystring_to_array(FastqTestCaseMixin.make_quality_scores(size=length))
+            qual = pysam.qualitystring_to_array(
+                FastqTestCaseMixin.make_quality_scores(size=length)
+            )
         segment.query_qualities = qual
 
         if tags is not None:
@@ -115,8 +119,7 @@ def make_bam_segment(
         return segment
 
     def make_bam(self, chroms, segments):
-        """
-        Make a synthetic BAM file.
+        """Make a synthetic BAM file.
 
         Each BAM file consists of header and alignment entries.
 

src/ngs_test_utils/testcase/bed.py

@@ -1,4 +1,5 @@
 """Test utilities for BED files."""
+
 import pybedtools as pbt
 
 

src/ngs_test_utils/testcase/fasta.py

@@ -1,4 +1,5 @@
 """Test utilities for FASTA files."""
+
 import os
 
 import numpy
@@ -16,7 +17,9 @@ def make_fasta_sequence(size, include_n=False, rnd_seed=None):
         bases = BASES + ["N"] if include_n else BASES
         return "".join(numpy.random.choice(bases, size))
 
-    def make_fasta(self, sequences=None, headers=None, num_sequences=10, seq_len=80, rnd_seed=None):
+    def make_fasta(
+        self, sequences=None, headers=None, num_sequences=10, seq_len=80, rnd_seed=None
+    ):
         """Make FASTA file."""
         if sequences and headers is None:
             num_sequences = len(sequences)
@@ -25,14 +28,14 @@ def make_fasta(self, sequences=None, headers=None, num_sequences=10, seq_len=80,
 
         numpy.random.seed(rnd_seed)
         if sequences is None:
-            random_seeds = numpy.random.randint(10 ** 5, size=num_sequences)
+            random_seeds = numpy.random.randint(10**5, size=num_sequences)
             sequences = [self.make_fasta_sequence(seq_len, rnd_seed=rnd) for rnd in random_seeds]
         if headers is None:
-            headers = ["{}".format(i + 1) for i in range(num_sequences)]
+            headers = [f"{i + 1}" for i in range(num_sequences)]
 
         out_file = self.get_filename(extension="fasta")
-        with open(out_file, "wt") as ofile:
-            for header, seq in zip(headers, sequences):
+        with open(out_file, "w") as ofile:
+            for header, seq in zip(headers, sequences, strict=False):
                 ofile.write(">" + header + "\n")
                 ofile.write(seq + "\n")
 

src/ngs_test_utils/testcase/fastq.py

@@ -1,4 +1,5 @@
 """Test utilities for FASTQ files."""
+
 import numpy
 
 from ngs_test_utils.base.fastq import FastqEntry
@@ -19,7 +20,7 @@ def make_sequence_id(self, rnd_seed=None):
         """Make sequence ID."""
         if rnd_seed:
             numpy.random.seed(rnd_seed)
-        return "random_sequence_{}".format(numpy.random.randint(0, 10 ** 4))
+        return f"random_sequence_{numpy.random.randint(0, 10**4)}"
 
     def make_fastq_entry(self, seq, seq_id=None, plus="+", quality=None, rnd_seed=None):
         """Make FASTQ entry."""
@@ -35,7 +36,7 @@ def make_fastq(self, entries):
         """Make FASTQ file from entries."""
         filename = self.get_filename(extension="fastq")
 
-        with open(filename, "wt") as ofile:
+        with open(filename, "w") as ofile:
             for entry in entries:
                 entry.write(ofile)
 

src/ngs_test_utils/testcase/gtf.py

@@ -1,4 +1,5 @@
 """Test utilities for GTF files."""
+
 import pybedtools as pbt
 
 
@@ -9,7 +10,7 @@ def create_gtf_attrs(self, **kwargs):
         """Create 9th column in GTF file - attributes."""
         attrs = ""
         for name, value in kwargs.items():
-            attrs += '{} "{}"; '.format(name, value)
+            attrs += f'{name} "{value}"; '
 
         attrs = attrs.strip()
         if attrs:

tests/test_bam.py

@@ -1,5 +1,3 @@
-import unittest
-
 import pysam
 
 from ngs_test_utils import testcase
@@ -36,5 +34,5 @@ def test_make_bam(self):
             self.assertEqual(bamfile.references, ("chr1", "chr2"))
             self.assertEqual(bamfile.mapped, 2)
             self.assertEqual(bamfile.unmapped, 1)
-            for read in bamfile.fetch():
+            for _ in bamfile.fetch():
                 pass

tests/test_fasta.py

@@ -1,5 +1,3 @@
-import unittest
-
 from ngs_test_utils import testcase
 
 
@@ -15,8 +13,17 @@ def test_make_fasta_sequence(self):
 
     def test_make_fasta(self):
         # headers=None, sequences=None
-        fasta = self.make_fasta(sequences=None, headers=None, num_sequences=3, seq_len=20, rnd_seed=42)
+        fasta = self.make_fasta(
+            sequences=None, headers=None, num_sequences=3, seq_len=20, rnd_seed=42
+        )
         self.assertEqual(
             self.tsv_to_list(fasta),
-            [[">1"], ["CATTATGCTCGATCAGGCCG"], [">2"], ["CTTTACGCCTTTCTTTGATG"], [">3"], ["CTTTGGGGCACTTAACTCCC"]],
+            [
+                [">1"],
+                ["CATTATGCTCGATCAGGCCG"],
+                [">2"],
+                ["CTTTACGCCTTTCTTTGATG"],
+                [">3"],
+                ["CTTTGGGGCACTTAACTCCC"],
+            ],
         )

tests/test_fastq.py

@@ -23,4 +23,6 @@ def test_make_fastq_entry(self):
     def test_make_fastq_file(self):
         entry = self.make_fastq_entry(seq="ACTG", rnd_seed=2)
         filename = self.make_fastq([entry])
-        self.assertEqual(self.tsv_to_list(filename), [["random_sequence_7336"], ["ACTG"], ["+"], ["I0)7"]])
+        self.assertEqual(
+            self.tsv_to_list(filename), [["random_sequence_7336"], ["ACTG"], ["+"], ["I0)7"]]
+        )