Apply 2026 black style

Author: nsoranzo

lib/bx/align/core.py

@@ -143,7 +143,7 @@ def slice_by_component(self, component_index, start, end):
         start_col = ref.coord_to_col(start)
         end_col = ref.coord_to_col(end)
         if ref.strand == "-":
-            (start_col, end_col) = (end_col, start_col)
+            start_col, end_col = (end_col, start_col)
         return self.slice(start_col, end_col)
 
     def column_iter(self):
@@ -355,7 +355,7 @@ def slice_by_coord(self, start, end):
         start_col = self.coord_to_col(start)
         end_col = self.coord_to_col(end)
         if self.strand == "-":
-            (start_col, end_col) = (end_col, start_col)
+            start_col, end_col = (end_col, start_col)
         return self.slice(start_col, end_col)
 
     def coord_to_col(self, pos):

lib/bx/align/lav.py

@@ -75,7 +75,7 @@ def __next__(self):
                 self.parse_h_stanza()
                 continue
             if line.startswith("a {"):
-                (score, pieces) = self.parse_a_stanza()
+                score, pieces = self.parse_a_stanza()
                 break
             if line.endswith("{"):
                 self.parse_unknown_stanza()
@@ -120,7 +120,7 @@ def open_seqs(self):
                     name1 = self.path_to_src_name(self.seq1_filename)
                 except ValueError:
                     name1 = "seq1"
-            (species1, chrom1) = src_split(name1)
+            species1, chrom1 = src_split(name1)
             self.seq1_src = src_merge(species1, chrom1, contig)
             if contig is not None:
                 chrom1 += f"[{contig}]"
@@ -152,7 +152,7 @@ def open_seqs(self):
                     name2 = self.path_to_src_name(self.seq2_filename)
                 except ValueError:
                     name2 = "seq2"
-            (species2, chrom2) = src_split(name2)
+            species2, chrom2 = src_split(name2)
             self.seq2_src = src_merge(species2, chrom2, contig)
             if contig is not None:
                 chrom2 += f"[{contig}]"
@@ -180,14 +180,10 @@ def close_seqs(self):
     def parse_s_stanza(self):
         self.close_seqs()
         line = self.fetch_line(report=" in s-stanza")
-        (self.seq1_filename, self.seq1_start, self.seq1_end, self.seq1_strand, self.seq1_contig) = self.parse_s_seq(
-            line
-        )
+        self.seq1_filename, self.seq1_start, self.seq1_end, self.seq1_strand, self.seq1_contig = self.parse_s_seq(line)
 
         line = self.fetch_line(report=" in s-stanza")
-        (self.seq2_filename, self.seq2_start, self.seq2_end, self.seq2_strand, self.seq2_contig) = self.parse_s_seq(
-            line
-        )
+        self.seq2_filename, self.seq2_start, self.seq2_end, self.seq2_strand, self.seq2_contig = self.parse_s_seq(line)
 
         line = self.fetch_line(report=" in s-stanza")
         assert line == "}", f'improper s-stanza terminator (line {self.lineNumber}, "{line}")'
@@ -467,7 +463,7 @@ def close(self):
         keys = list(self.blockHash)
         keys = sort_keys_by_chrom(keys)
         for key in keys:
-            (src1, strand1, src2, strand2) = key
+            src1, strand1, src2, strand2 = key
             alignment = self.blockHash[key][0]
             self.src1 = src1
             self.strand1 = strand1
@@ -485,8 +481,8 @@ def close(self):
 
     def write_s_stanza(self):
         self.write_lav_marker()
-        (strand1, flag1) = minus_or_nothing(self.strand1)
-        (strand2, flag2) = minus_or_nothing(self.strand2)
+        strand1, flag1 = minus_or_nothing(self.strand1)
+        strand2, flag2 = minus_or_nothing(self.strand2)
         fname1 = build_filename(self.fname1, self.src1)
         fname2 = build_filename(self.fname2, self.src2)
         print("s {", file=self.file)
@@ -522,7 +518,7 @@ def write_a_stanza(self, alignment):
             nonGap = (ch1 != "-") and (ch2 != "-")
             if nonGap:
                 if piece1 is None:  # new piece starts
-                    (piece1, piece2, idCount) = (pos1, pos2, 0)
+                    piece1, piece2, idCount = (pos1, pos2, 0)
                 if ch1 == ch2:
                     idCount += 1
             elif piece1 is not None:  # new gap starts
@@ -543,11 +539,11 @@ def write_a_stanza(self, alignment):
 
         # write the block
 
-        (start1, start2, size, pctId) = pieces[-1]  # get end of final piece
+        start1, start2, size, pctId = pieces[-1]  # get end of final piece
         end1 = start1 + size
         end2 = start2 + size
 
-        (start1, start2, size, pctId) = pieces[0]  # get start of first piece
+        start1, start2, size, pctId = pieces[0]  # get start of first piece
 
         score = int(round(alignment.score))
 
@@ -575,7 +571,7 @@ def sort_keys_by_chrom(keys):
 
 
 def chrom_key(src):
-    (species, chrom) = src_split(src)
+    species, chrom = src_split(src)
     if chrom.startswith("chr"):
         chrom = chrom[3:]
     try:
@@ -591,7 +587,7 @@ def build_filename(fmt, src):
     num = fmt.count("%s")
     if num == 0:
         return fmt
-    (species, chrom) = src_split(src)
+    species, chrom = src_split(src)
     if num == 1:
         return fmt % chrom
     return fmt % (species, chrom)

lib/bx/align/maf_tests.py

@@ -120,15 +120,12 @@ def test_writer():
 
     writer.write(a)
 
-    assert (
-        val.getvalue()
-        == """##maf version=1 scoring=foobar
+    assert val.getvalue() == """##maf version=1 scoring=foobar
 a score=7009
 s human_hoxa 100  9 + 1000257 ACA-TTACT 
 s horse_hoxa 120 10 -   98892 ACAATTGCT 
 
 """  # noqa: W291
-    )
 
 
 def test_slice():

lib/bx/align/score.py

@@ -48,11 +48,11 @@ def __init__(
         # implement a different underlying table object
 
     def _set_score(self, a_b_pair, val):
-        (a, b) = a_b_pair
+        a, b = a_b_pair
         self.table[a, b] = val
 
     def _get_score(self, a_b_pair):
-        (a, b) = a_b_pair
+        a, b = a_b_pair
         return self.table[a, b]
 
     def set_score(self, a, b, val, foldcase1=False, foldcase2=False):

lib/bx/pwm/position_weight_matrix.py

@@ -210,7 +210,7 @@ def __init__(self, id, rows, alphabet, background=None, score_correction=True):
             fields, consensus = rows[i][:nsymbols], rows[i][-1]
             for x, count in enumerate(fields):
                 try:
-                    (w, s) = self.parse_weight(count)
+                    w, s = self.parse_weight(count)
                 except ValueError:
                     raise ValueError("pwm row {} has bad weight {}".format(" ".join(fields), w))
 
@@ -229,7 +229,7 @@ def __init__(self, id, rows, alphabet, background=None, score_correction=True):
         for i in range(len(rows)):
             hashRows.append({})
             for x, sym in enumerate(alphabet):
-                (w, s) = rows[i][x]
+                w, s = rows[i][x]
                 hashRows[i][sym] = w * scale / s
                 assert hashRows[i][sym] >= 0
                 if sym not in self.matrix_base_counts:

lib/bx/seq/fasta.py

@@ -50,7 +50,7 @@ def __init__(self, file, revcomp=False, name="", gap=None, lookahead=None, conti
         currContig = 1
         while True:
             if self.lookahead is not None:
-                (line, self.lookahead) = (self.lookahead, None)
+                line, self.lookahead = (self.lookahead, None)
             else:
                 line = self.file.readline()
                 if not isinstance(line, str):

lib/bx/seq/qdna.py

@@ -169,7 +169,7 @@ def __next__(self):
 
 class QdnaCodebook:
     def __init__(self, file):
-        (self.alphabet, self.codeToProbs) = self.read_codebook(file)
+        self.alphabet, self.codeToProbs = self.read_codebook(file)
 
     def __str__(self):
         codeSet = sorted(codeNum for codeNum in self.codeToProbs)

lib/bx_extras/stats.py

@@ -154,6 +154,7 @@
                     outputpairedstats
                     findwithin
 """
+
 # CHANGE LOG:
 # ===========
 # 02-11-19 ... fixed attest_ind and attest_rel for div-by-zero Overflows
@@ -300,7 +301,7 @@ def lmedian(inlist, numbins=1000):
     Heiman's Basic Stats (1st Edition), or CRC Probability & Statistics.
 
     Usage:   lmedian (inlist, numbins=1000)"""
-    (hist, smallest, binsize, extras) = histogram(inlist, numbins)  # make histog
+    hist, smallest, binsize, extras = histogram(inlist, numbins)  # make histog
     cumhist = cumsum(hist)  # make cumulative histogram
     for i in range(len(cumhist)):  # get 1st(!) index holding 50%ile score
         if cumhist[i] >= len(inlist) / 2.0:
@@ -2217,7 +2218,7 @@ def amedian(inarray, numbins=1000):
         Returns: median calculated over ALL values in inarray
         """
         inarray = N.ravel(inarray)
-        (hist, smallest, binsize, extras) = ahistogram(inarray, numbins)
+        hist, smallest, binsize, extras = ahistogram(inarray, numbins)
         cumhist = N.cumsum(hist)  # make cumulative histogram
         otherbins = N.greater_equal(cumhist, len(inarray) / 2.0)
         otherbins = list(otherbins)  # list of 0/1s, 1s start at median bin

script_tests/line_select_tests.py

@@ -5,24 +5,18 @@
 
 class Test(base.BaseScriptTest, unittest.TestCase):
     command_line = "./scripts/line_select.py ${features}"
-    input_features = base.TestFile(
-        """0
+    input_features = base.TestFile("""0
                                        1
                                        1
                                        0
                                        1
-                                       0"""
-    )
-    input_stdin = base.TestFile(
-        """a
+                                       0""")
+    input_stdin = base.TestFile("""a
                                     b
 
                                     d
                                     e
-                                    f"""
-    )
-    output_stdout = base.TestFile(
-        """b
+                                    f""")
+    output_stdout = base.TestFile("""b
 
-                                      e"""
-    )
+                                      e""")

script_tests/maf_select_tests.py

@@ -5,31 +5,27 @@
 
 class Test(base.BaseScriptTest, unittest.TestCase):
     command_line = "./scripts/maf_select.py ${features}"
-    input_features = base.TestFile(
-        """0
+    input_features = base.TestFile("""0
                                        0
                                        0
                                        0
                                        0
                                        0
                                        0
-                                       1"""
-    )
+                                       1""")
     input_stdin = base.TestFile(filename="./test_data/maf_tests/mm8_chr7_tiny_no_index.maf")
     output_stdout = base.TestFile(filename="./test_data/maf_tests/mm8_chr7_tiny_last_selected.maf")
 
 
 class TestWithE(base.BaseScriptTest, unittest.TestCase):
     command_line = "./scripts/maf_select.py ${features}"
-    input_features = base.TestFile(
-        """0
+    input_features = base.TestFile("""0
                                        1
                                        0
                                        0
                                        0
                                        0
                                        0
-                                       0"""
-    )
+                                       0""")
     input_stdin = base.TestFile(filename="./test_data/maf_tests/mm10_chr12_lessspe.maf")
     output_stdout = base.TestFile(filename="./test_data/maf_tests/mm10_chr12_lessspe_one_selected.maf")