diff --git a/jcvi/annotation/depth.py b/jcvi/annotation/depth.py
index 42fa1945..2fbd8971 100755
--- a/jcvi/annotation/depth.py
+++ b/jcvi/annotation/depth.py
@@ -25,7 +25,7 @@ class BinFile(BaseFile):
     """
 
     def __init__(self, binfile, dtype=np.uint8):
-        super(BinFile, self).__init__(binfile)
+        super().__init__(binfile)
         assert op.exists(
             binfile
         ), "Binary file `{0}` not found. Rerun depth.count().".format(binfile)
diff --git a/jcvi/annotation/maker.py b/jcvi/annotation/maker.py
index c0e50216..bdb7c139 100644
--- a/jcvi/annotation/maker.py
+++ b/jcvi/annotation/maker.py
@@ -59,7 +59,7 @@ def __str__(self):
 
 class CTLFile(LineFile):
     def __init__(self, filename):
-        super(CTLFile, self).__init__(filename)
+        super().__init__(filename)
         fp = open(filename)
         for row in fp:
             self.append(CTLine(row))
@@ -90,7 +90,7 @@ def write_file(self, filename):
 
 class DatastoreIndexFile(BaseFile):
     def __init__(self, filename):
-        super(DatastoreIndexFile, self).__init__(filename)
+        super().__init__(filename)
         scaffold_status = {}
         failed = []
 
diff --git a/jcvi/apps/base.py b/jcvi/apps/base.py
index a519f764..cdee0853 100644
--- a/jcvi/apps/base.py
+++ b/jcvi/apps/base.py
@@ -139,7 +139,7 @@ class OptionParser(ArgumentParser):
 
     def __init__(self, doc: Optional[str]):
         usage = doc.replace("%prog", "%(prog)s") if doc else None
-        super(OptionParser, self).__init__(usage=usage, epilog=JCVIHELP)
+        super().__init__(usage=usage, epilog=JCVIHELP)
 
     def parse_args(self, args=None):
         """
diff --git a/jcvi/apps/bowtie.py b/jcvi/apps/bowtie.py
index 1fb266fc..bf626b0f 100644
--- a/jcvi/apps/bowtie.py
+++ b/jcvi/apps/bowtie.py
@@ -40,7 +40,7 @@ class BowtieLogFile(BaseFile):
 
     def __init__(self, filename):
 
-        super(BowtieLogFile, self).__init__(filename)
+        super().__init__(filename)
         fp = open(filename)
         self.total = int(first_tag(fp))
         self.unpaired = int(first_tag(fp))
diff --git a/jcvi/apps/cdhit.py b/jcvi/apps/cdhit.py
index 0bbc0940..0a20e228 100644
--- a/jcvi/apps/cdhit.py
+++ b/jcvi/apps/cdhit.py
@@ -35,7 +35,7 @@ def __init__(self, row):
 
 class ClstrFile(LineFile):
     def __init__(self, filename):
-        super(ClstrFile, self).__init__(filename)
+        super().__init__(filename)
         assert filename.endswith(".clstr")
 
         fp = open(filename)
diff --git a/jcvi/apps/grid.py b/jcvi/apps/grid.py
index 81f4859a..5a3a3b4f 100644
--- a/jcvi/apps/grid.py
+++ b/jcvi/apps/grid.py
@@ -73,16 +73,16 @@ class Queue(Queue):
     """
 
     def __init__(self, *args, **kwargs):
-        super(Queue, self).__init__(*args, **kwargs, ctx=get_context())
+        super().__init__(*args, **kwargs, ctx=get_context())
         self.size = SharedCounter(0)
 
     def put(self, *args, **kwargs):
         self.size.increment(1)
-        super(Queue, self).put(*args, **kwargs)
+        super().put(*args, **kwargs)
 
     def get(self, *args, **kwargs):
         self.size.increment(-1)
-        return super(Queue, self).get(*args, **kwargs)
+        return super().get(*args, **kwargs)
 
     def qsize(self):
         """Reliable implementation of multiprocessing.Queue.qsize()"""
diff --git a/jcvi/apps/uclust.py b/jcvi/apps/uclust.py
index 3620b4d8..1da53f33 100644
--- a/jcvi/apps/uclust.py
+++ b/jcvi/apps/uclust.py
@@ -66,7 +66,7 @@
 
 class ClustFile(BaseFile):
     def __init__(self, filename):
-        super(ClustFile, self).__init__(filename)
+        super().__init__(filename)
 
     def __iter__(self):
         nstacks = 0
@@ -87,7 +87,7 @@ def __iter__(self):
 
 class Clust(list):
     def __init__(self):
-        super(Clust, self).__init__(self)
+        super().__init__(self)
 
     def __str__(self):
         s = []
@@ -98,7 +98,7 @@ def __str__(self):
 
 class ClustStore(BaseFile):
     def __init__(self, consensfile):
-        super(ClustStore, self).__init__(consensfile)
+        super().__init__(consensfile)
         binfile = consensfile + ".bin"
         idxfile = consensfile + ".idx"
         self.bin = np.fromfile(binfile, dtype=np.uint16)
@@ -180,7 +180,7 @@ class ClustStores(dict):
     """
 
     def __init__(self, consensfiles):
-        super(ClustStores, self).__init__(self)
+        super().__init__(self)
         for cs in consensfiles:
             name = op.basename(cs).split(".")[0]
             self[name] = ClustStore(cs)
diff --git a/jcvi/assembly/allmaps.py b/jcvi/assembly/allmaps.py
index 9eaa285e..575554ce 100644
--- a/jcvi/assembly/allmaps.py
+++ b/jcvi/assembly/allmaps.py
@@ -515,7 +515,7 @@ def __init__(
         remove_outliers=False,
         function=(lambda x: x.rank),
     ):
-        super(Map, self).__init__()
+        super().__init__()
         bed = Bed(filename)
         for b in bed:
             self.append(Marker(b))
@@ -635,7 +635,7 @@ def export_table(self, r, mapname, total):
 
 class Weights(DictFile):
     def __init__(self, filename, mapnames, cast=int):
-        super(Weights, self).__init__(filename, cast=cast)
+        super().__init__(filename, cast=cast)
         self.maps = [x.split()[0] for x in must_open(filename)]
         self.update_maps(mapnames)
         pivot_weight, o, pivot = self.get_pivot(mapnames)
diff --git a/jcvi/assembly/allpaths.py b/jcvi/assembly/allpaths.py
index 4575a551..e95c3e18 100644
--- a/jcvi/assembly/allpaths.py
+++ b/jcvi/assembly/allpaths.py
@@ -29,7 +29,7 @@
 
 class PairsFile(BaseFile):
     def __init__(self, filename):
-        super(PairsFile, self).__init__(filename)
+        super().__init__(filename)
 
         fp = open(filename, "rb")
         (binwrite,) = unpack("8s", fp.read(8))
diff --git a/jcvi/assembly/automaton.py b/jcvi/assembly/automaton.py
index 3a71130b..08ca0153 100644
--- a/jcvi/assembly/automaton.py
+++ b/jcvi/assembly/automaton.py
@@ -73,7 +73,7 @@ def guess(self):
 
 class MetaFile(LineFile):
     def __init__(self, filename):
-        super(MetaFile, self).__init__(filename)
+        super().__init__(filename)
         fp = open(filename)
         for row in fp:
             genome, tag, fastq = row.split()
diff --git a/jcvi/assembly/coverage.py b/jcvi/assembly/coverage.py
index 9dfa17bc..da5aab99 100644
--- a/jcvi/assembly/coverage.py
+++ b/jcvi/assembly/coverage.py
@@ -34,7 +34,7 @@ def __init__(self, bedfile, sizesfile):
 
         filename = coveragefile
         assert filename.endswith(".coverage")
-        super(Coverage, self).__init__(filename)
+        super().__init__(filename)
 
     def get_plot_data(self, ctg, bins=None):
         import numpy as np
diff --git a/jcvi/assembly/geneticmap.py b/jcvi/assembly/geneticmap.py
index d09c96b1..2720c3ae 100644
--- a/jcvi/assembly/geneticmap.py
+++ b/jcvi/assembly/geneticmap.py
@@ -47,7 +47,7 @@
 
 class BinMap(BaseFile, dict):
     def __init__(self, filename):
-        super(BinMap, self).__init__(filename)
+        super().__init__(filename)
 
         fp = open(filename)
         for header, seq in read_block(fp, "group "):
@@ -111,7 +111,7 @@ def bedline(self):
 
 class MSTMap(LineFile):
     def __init__(self, filename):
-        super(MSTMap, self).__init__(filename)
+        super().__init__(filename)
         fp = open(filename)
         startidx = 1
         for row in fp:
diff --git a/jcvi/assembly/goldenpath.py b/jcvi/assembly/goldenpath.py
index ee71b2c3..5108a5c6 100644
--- a/jcvi/assembly/goldenpath.py
+++ b/jcvi/assembly/goldenpath.py
@@ -357,7 +357,7 @@ class Certificate(BaseFile):
 
     def __init__(self, filename):
 
-        super(Certificate, self).__init__(filename)
+        super().__init__(filename)
 
         fp = open(filename)
         self.lines = [CertificateLine(x) for x in fp.readlines()]
diff --git a/jcvi/assembly/hic.py b/jcvi/assembly/hic.py
index 9169b40a..f4392b88 100644
--- a/jcvi/assembly/hic.py
+++ b/jcvi/assembly/hic.py
@@ -84,7 +84,7 @@ class ContigOrdering(LineFile):
     """
 
     def __init__(self, filename):
-        super(ContigOrdering, self).__init__(filename)
+        super().__init__(filename)
         fp = open(filename)
         for row in fp:
             if row[0] == "#":
diff --git a/jcvi/assembly/kmer.py b/jcvi/assembly/kmer.py
index 9f43c2a4..f50d69ca 100644
--- a/jcvi/assembly/kmer.py
+++ b/jcvi/assembly/kmer.py
@@ -48,7 +48,7 @@
 
 class KmerSpectrum(BaseFile):
     def __init__(self, histfile):
-        super(KmerSpectrum, self).__init__(histfile)
+        super().__init__(histfile)
         self.load_data(histfile)
 
     def load_data(self, histfile):
diff --git a/jcvi/assembly/preprocess.py b/jcvi/assembly/preprocess.py
index 849279c6..54b7659f 100644
--- a/jcvi/assembly/preprocess.py
+++ b/jcvi/assembly/preprocess.py
@@ -26,7 +26,7 @@
 
 class FastQCdata(BaseFile, dict):
     def __init__(self, filename, human=False):
-        super(FastQCdata, self).__init__(filename)
+        super().__init__(filename)
         if not op.exists(filename):
             logger.debug("File `%s` not found.", filename)
             # Sample_RF37-1/RF37-1_GATCAG_L008_R2_fastqc =>
diff --git a/jcvi/assembly/syntenypath.py b/jcvi/assembly/syntenypath.py
index 7d12d24f..82fa9a84 100644
--- a/jcvi/assembly/syntenypath.py
+++ b/jcvi/assembly/syntenypath.py
@@ -44,7 +44,7 @@ def tag(self):
 
 class OVL(LineFile):
     def __init__(self, filename):
-        super(OVL, self).__init__(filename)
+        super().__init__(filename)
         fp = must_open(filename)
         contained = set()
         alledges = defaultdict(list)
diff --git a/jcvi/compara/base.py b/jcvi/compara/base.py
index eae6ec6b..6cec765a 100644
--- a/jcvi/compara/base.py
+++ b/jcvi/compara/base.py
@@ -7,7 +7,7 @@
 
 class AnchorFile(BaseFile):
     def __init__(self, filename, minsize=0):
-        super(AnchorFile, self).__init__(filename)
+        super().__init__(filename)
         self.blocks = list(self.iter_blocks(minsize=minsize))
 
     def iter_blocks(self, minsize=0):
diff --git a/jcvi/compara/catalog.py b/jcvi/compara/catalog.py
index f98573a0..fe2d4247 100644
--- a/jcvi/compara/catalog.py
+++ b/jcvi/compara/catalog.py
@@ -39,7 +39,7 @@
 
 class OMGFile(BaseFile):
     def __init__(self, filename):
-        super(OMGFile, self).__init__(filename)
+        super().__init__(filename)
         fp = open(filename)
         inblock = False
         components = []
diff --git a/jcvi/compara/ks.py b/jcvi/compara/ks.py
index a26fe93a..2dfcf3e3 100644
--- a/jcvi/compara/ks.py
+++ b/jcvi/compara/ks.py
@@ -159,7 +159,7 @@ def __str__(self):
 
 class Layout(AbstractLayout):
     def __init__(self, filename, delimiter=",", seed: Optional[int] = None):
-        super(Layout, self).__init__(filename)
+        super().__init__(filename)
         if not op.exists(filename):
             ksfiles = iglob(".", "*.ks")
             header = "Ks file|ncomponents|label|color|marker".split("|")
@@ -934,7 +934,7 @@ def anchorline(self):
 
 class KsFile(LineFile):
     def __init__(self, filename, strip_names=False):
-        super(KsFile, self).__init__(filename)
+        super().__init__(filename)
 
         fp = open(filename)
         for row in fp:
diff --git a/jcvi/compara/synteny.py b/jcvi/compara/synteny.py
index 31c6a941..b039ba87 100755
--- a/jcvi/compara/synteny.py
+++ b/jcvi/compara/synteny.py
@@ -28,7 +28,7 @@ class BlockFile(BaseFile):
     """Parse .blocks file which is the mcscan output with multiple columns as 'tracks'"""
 
     def __init__(self, filename, defaultcolor="#fb8072", header=False):
-        super(BlockFile, self).__init__(filename)
+        super().__init__(filename)
         fp = must_open(filename)
         hd = next(fp).rstrip().split("\t")
         ncols = len(hd)
diff --git a/jcvi/formats/agp.py b/jcvi/formats/agp.py
index dd9b8180..58c79362 100644
--- a/jcvi/formats/agp.py
+++ b/jcvi/formats/agp.py
@@ -286,7 +286,7 @@ def gline(cls, object, gap, unknown=100):
 
 class AGP(LineFile):
     def __init__(self, filename, nogaps=False, validate=True, sorted=True):
-        super(AGP, self).__init__(filename)
+        super().__init__(filename)
 
         fp = must_open(filename)
         self.header = []
@@ -653,7 +653,7 @@ def isCloneGap(self):
 
 class TPF(LineFile):
     def __init__(self, filename):
-        super(TPF, self).__init__(filename)
+        super().__init__(filename)
         fp = open(filename)
         for row in fp:
             if row[0] == "#":
@@ -693,7 +693,7 @@ def __init__(self, id, component_id, component_size, strand):
 
 class OO(LineFile):
     def __init__(self, filename=None, ctgsizes=None):
-        super(OO, self).__init__(filename)
+        super().__init__(filename)
 
         if filename is None:
             return
diff --git a/jcvi/formats/base.py b/jcvi/formats/base.py
index f155fd94..f711b9ea 100644
--- a/jcvi/formats/base.py
+++ b/jcvi/formats/base.py
@@ -42,7 +42,7 @@ class LineFile(BaseFile, list):
     """
 
     def __init__(self, filename, comment=None, load=False):
-        super(LineFile, self).__init__(filename)
+        super().__init__(filename)
 
         if load:
             fp = must_open(filename)
@@ -117,7 +117,7 @@ def num_columns(cls, filename, delimiter=None):
 
 class SetFile(BaseFile, set):
     def __init__(self, filename, column=-1, delimiter=None):
-        super(SetFile, self).__init__(filename)
+        super().__init__(filename)
         fp = open(filename)
         for row in fp:
             if not row.strip():
diff --git a/jcvi/formats/bed.py b/jcvi/formats/bed.py
index 3b361579..eb6886f5 100755
--- a/jcvi/formats/bed.py
+++ b/jcvi/formats/bed.py
@@ -143,7 +143,7 @@ def gffline(self, type="match", source="default"):
 
 class Bed(LineFile):
     def __init__(self, filename=None, key=None, sorted=True, juncs=False, include=None):
-        super(Bed, self).__init__(filename)
+        super().__init__(filename)
 
         # the sorting key provides some flexibility in ordering the features
         # for example, user might not like the lexico-order of seqid
diff --git a/jcvi/formats/blast.py b/jcvi/formats/blast.py
index e03b55e5..75de55f6 100644
--- a/jcvi/formats/blast.py
+++ b/jcvi/formats/blast.py
@@ -35,7 +35,7 @@ class BlastSlow(LineFile):
     """
 
     def __init__(self, filename, sorted=False):
-        super(BlastSlow, self).__init__(filename)
+        super().__init__(filename)
         fp = must_open(filename)
         for row in fp:
             self.append(BlastLine(row))
@@ -75,7 +75,7 @@ class Blast(BaseFile):
     """
 
     def __init__(self, filename):
-        super(Blast, self).__init__(filename)
+        super().__init__(filename)
         self.fp = must_open(filename)
 
     def __iter__(self):
@@ -141,7 +141,7 @@ class BlastLineByConversion(BlastLine):
 
     def __init__(self, sline, mode="1" * 12):
         if int(mode, 2) == 4095:
-            super(BlastLineByConversion, self).__init__(sline)
+            super().__init__(sline)
         elif 3072 <= int(mode, 2) < 4095:
             args = sline.split("\t")
             atoms = args[:2]
@@ -159,7 +159,7 @@ def __init__(self, sline, mode="1" * 12):
                     else:
                         atoms.append("-1")
             sline = "\t".join(atoms)
-            super(BlastLineByConversion, self).__init__(sline)
+            super().__init__(sline)
         else:
             m = "mode can only contain 0 or 1 \n"
             m += "first two fields (query, subject) cannot be empty"
diff --git a/jcvi/formats/cdt.py b/jcvi/formats/cdt.py
index e5a1173f..077b34f4 100644
--- a/jcvi/formats/cdt.py
+++ b/jcvi/formats/cdt.py
@@ -23,7 +23,7 @@
 
 class CDT(BaseFile):
     def __init__(self, filename):
-        super(CDT, self).__init__(filename)
+        super().__init__(filename)
 
         pf = filename.rsplit(".", 1)[0]
         self.gtrfile = pf + ".gtr"
diff --git a/jcvi/formats/chain.py b/jcvi/formats/chain.py
index 732f8c56..4f4f0d96 100644
--- a/jcvi/formats/chain.py
+++ b/jcvi/formats/chain.py
@@ -52,7 +52,7 @@ def __init__(self, chain, lines):
 
 class Chain(BaseFile):
     def __init__(self, filename):
-        super(Chain, self).__init__(filename)
+        super().__init__(filename)
         self.chains = list(self.iter_chain())
 
         self.ungapped = sum(x.ungapped for x in self.chains)
diff --git a/jcvi/formats/contig.py b/jcvi/formats/contig.py
index e3d87d1c..48882e0d 100644
--- a/jcvi/formats/contig.py
+++ b/jcvi/formats/contig.py
@@ -64,7 +64,7 @@ def __str__(self):
 
 class ContigFile(BaseFile):
     def __init__(self, filename):
-        super(ContigFile, self).__init__(filename)
+        super().__init__(filename)
         self.fp = open(filename)
 
     def iter_records(self):
diff --git a/jcvi/formats/coords.py b/jcvi/formats/coords.py
index c0aeca09..03596620 100644
--- a/jcvi/formats/coords.py
+++ b/jcvi/formats/coords.py
@@ -192,7 +192,7 @@ def __init__(self, filename, sorted=False, header=False):
                 fromdelta([filename])
             filename = coordsfile
 
-        super(Coords, self).__init__(filename)
+        super().__init__(filename)
 
         fp = open(filename)
         if header:
diff --git a/jcvi/formats/fasta.py b/jcvi/formats/fasta.py
index e78b38f7..3846609c 100644
--- a/jcvi/formats/fasta.py
+++ b/jcvi/formats/fasta.py
@@ -29,7 +29,7 @@
 
 class Fasta(BaseFile, dict):
     def __init__(self, filename, index=False, key_function=None, lazy=False):
-        super(Fasta, self).__init__(filename)
+        super().__init__(filename)
         self.key_function = key_function
 
         if lazy:  # do not incur the overhead
diff --git a/jcvi/formats/genbank.py b/jcvi/formats/genbank.py
index cec25a11..28a85e22 100644
--- a/jcvi/formats/genbank.py
+++ b/jcvi/formats/genbank.py
@@ -29,7 +29,7 @@ class MultiGenBank(BaseFile):
     """
 
     def __init__(self, filename, source="JCVI"):
-        super(MultiGenBank, self).__init__(filename)
+        super().__init__(filename)
         assert op.exists(filename)
 
         pf = filename.rsplit(".", 1)[0]
diff --git a/jcvi/formats/gff.py b/jcvi/formats/gff.py
index 88c09e2b..36f8faf5 100644
--- a/jcvi/formats/gff.py
+++ b/jcvi/formats/gff.py
@@ -325,7 +325,7 @@ def __init__(
         make_gff_store=False,
         compute_signature=False,
     ):
-        super(Gff, self).__init__(filename)
+        super().__init__(filename)
         self.make_gff_store = make_gff_store
         self.gff3 = True
         if self.make_gff_store:
diff --git a/jcvi/formats/maf.py b/jcvi/formats/maf.py
index 4317d5ab..3084a77c 100644
--- a/jcvi/formats/maf.py
+++ b/jcvi/formats/maf.py
@@ -18,7 +18,7 @@
 
 class Maf(BaseFile, dict):
     def __init__(self, filename, index=False):
-        super(Maf, self).__init__(filename)
+        super().__init__(filename)
 
         indexfile = filename + ".idx"
         if index:
diff --git a/jcvi/formats/psl.py b/jcvi/formats/psl.py
index 5b0af407..df1774c8 100755
--- a/jcvi/formats/psl.py
+++ b/jcvi/formats/psl.py
@@ -254,10 +254,7 @@ def bed12line(self):
 
 class Psl(LineFile):
     def __init__(self, filename=None):
-        super(Psl, self).__init__(filename)
-
-        import re
-
+        super().__init__(filename)
         self.mCounts = {}  # dict to hold match counts
         if not filename:
             return
diff --git a/jcvi/formats/sam.py b/jcvi/formats/sam.py
index a9c59ca0..01b4d904 100644
--- a/jcvi/formats/sam.py
+++ b/jcvi/formats/sam.py
@@ -93,7 +93,7 @@ def pairline(self):
 
 class Sam(LineFile):
     def __init__(self, filename, callback=None):
-        super(Sam, self).__init__(filename)
+        super().__init__(filename)
         fp = open(filename)
         for row in fp:
             if row[0] == "@":
@@ -126,7 +126,7 @@ def __init__(self, row):
 
 class GenomeCoverageFile(LineFile):
     def __init__(self, filename):
-        super(GenomeCoverageFile, self).__init__(filename)
+        super().__init__(filename)
         fp = open(filename)
         for row in fp:
             self.append(GenomeCoverageLine(row))
diff --git a/jcvi/formats/sizes.py b/jcvi/formats/sizes.py
index 92db1001..c2817eaf 100644
--- a/jcvi/formats/sizes.py
+++ b/jcvi/formats/sizes.py
@@ -44,7 +44,7 @@ def __init__(self, filename, select=None):
 
         assert filename.endswith(".sizes")
 
-        super(Sizes, self).__init__(filename)
+        super().__init__(filename)
         self.fp = open(filename)
         self.filename = filename
 
diff --git a/jcvi/graphics/align.py b/jcvi/graphics/align.py
index 7328b905..a8ab05a7 100644
--- a/jcvi/graphics/align.py
+++ b/jcvi/graphics/align.py
@@ -74,7 +74,7 @@ def duplicate(self, a, b, gap=0):
 
 class PairwiseAlign(BaseAlign):
     def __init__(self, fig, xywh, xpad=0.15, ypad=0.15):
-        super(PairwiseAlign, self).__init__(fig, xywh, xpad, ypad)
+        super().__init__(fig, xywh, xpad, ypad)
 
     def draw(self, width=0.03):
         HorizontalChromosome(
@@ -107,7 +107,7 @@ def draw(self, width=0.03):
 
 class ReadAlign(BaseAlign):
     def __init__(self, fig, xywh, xpad=0.05, ypad=0.2, readlen=6, gap=3):
-        super(ReadAlign, self).__init__(fig, xywh, xpad, ypad)
+        super().__init__(fig, xywh, xpad, ypad)
         self.readlen = readlen
         self.gap = gap
         self.reads = []
@@ -214,7 +214,7 @@ def duplicate(self, a, b, gap=0):
 
 class OpticalMapAlign(BaseAlign):
     def __init__(self, fig, xywh, xpad=0.05, ypad=0.3):
-        super(OpticalMapAlign, self).__init__(fig, xywh, xpad, ypad)
+        super().__init__(fig, xywh, xpad, ypad)
         om = self.from_silico()
         self.om1 = OpticalMapTrack(self.sax, om)
         self.om2 = OpticalMapTrack(self.sax, om, ystart=-3, color="orange")
@@ -263,7 +263,7 @@ def duplicate(self, a, b, gap=0):
 class OpticalMapTrack(BaseGlyph):
     def __init__(self, ax, sizes, ystart=0, color="darkslategrey", height=1, wiggle=3):
 
-        super(OpticalMapTrack, self).__init__(ax)
+        super().__init__(ax)
         self.ax = ax
         self.sizes = sizes[:]
         self.ystart = ystart
diff --git a/jcvi/graphics/base.py b/jcvi/graphics/base.py
index c956b3ba..6b40aa45 100644
--- a/jcvi/graphics/base.py
+++ b/jcvi/graphics/base.py
@@ -129,7 +129,7 @@ class AbstractLayout(LineFile):
     """
 
     def __init__(self, filename):
-        super(AbstractLayout, self).__init__(filename)
+        super().__init__(filename)
 
     def assign_array(self, attrib, array):
         assert len(array) == len(self)
@@ -708,7 +708,7 @@ def draw_cmap(ax, cmap_text, vmin, vmax, cmap=None, reverse=False):
         ax.text(x, ymin - 0.005, "%.1f" % v, ha="center", va="top", size=10)
 
 
-def write_messages(ax, messages: List[str], ypad: float=0.04):
+def write_messages(ax, messages: List[str], ypad: float = 0.04):
     """
     Write text on canvas, usually on the top right corner.
     """
diff --git a/jcvi/graphics/chromosome.py b/jcvi/graphics/chromosome.py
index 10a7ba39..6aa6fada 100644
--- a/jcvi/graphics/chromosome.py
+++ b/jcvi/graphics/chromosome.py
@@ -60,7 +60,7 @@ def __init__(
         alternating shades. Use a list of starting locations to segment.
         """
         y1, y2 = sorted((y1, y2))
-        super(Chromosome, self).__init__(ax)
+        super().__init__(ax)
         pts, r = self.get_pts(x, y1, y2, width)
         self.append(Polygon(pts, fill=False, lw=lw, ec=ec, zorder=zorder))
         if patch:
@@ -112,7 +112,7 @@ def __init__(
         assert style in Chromosome.Styles, f"Unknown style `{style}`"
 
         x1, x2 = sorted((x1, x2))
-        super(HorizontalChromosome, self).__init__(ax)
+        super().__init__(ax)
         pts, r = self.get_pts(x1, x2, y, height, style=style)
         self.append(Polygon(pts, fill=False, lw=lw, ec=ec, zorder=zorder + 1))
 
@@ -235,7 +235,7 @@ class GeneticMap(BaseGlyph):
     def __init__(
         self, ax, x, y1, y2, markers, unit="cM", tip=0.008, fc="k", flip=False
     ):
-        super(GeneticMap, self).__init__(ax)
+        super().__init__(ax)
         # tip = length of the ticks
         y1, y2 = sorted((y1, y2))
         ax.plot([x, x], [y1, y2], "-", color=fc, lw=2)
@@ -285,7 +285,7 @@ def __init__(
             extra (float): offset for the unit label
             fc (str): face color of the glyph
         """
-        super(Gauge, self).__init__(ax)
+        super().__init__(ax)
         ax.plot([x, x], [y1, y2], "-", color=fc, lw=2)
         r = y2 - y1
         yy = y2
diff --git a/jcvi/graphics/dotplot.py b/jcvi/graphics/dotplot.py
index e761f754..90d6c2d1 100755
--- a/jcvi/graphics/dotplot.py
+++ b/jcvi/graphics/dotplot.py
@@ -61,7 +61,7 @@ def __init__(self, palettedict=None, palettefile=None):
             palettedict (Dict, optional): Get the mapping from a dict. Defaults to None.
             palettefile (str, optional): Get the mapping from a two-column file. Defaults to None.
         """
-        super(Palette, self).__init__()
+        super().__init__()
         if palettedict is not None:
             self.update(palettedict)
         if palettefile is None:
diff --git a/jcvi/graphics/glyph.py b/jcvi/graphics/glyph.py
index dfc1accf..d6de01a1 100644
--- a/jcvi/graphics/glyph.py
+++ b/jcvi/graphics/glyph.py
@@ -288,7 +288,7 @@ def __init__(
             style (str, optional): Style, either box|arrow. Defaults to "box".
         """
 
-        super(Glyph, self).__init__(ax)
+        super().__init__(ax)
         width = x2 - x1
         # Frame around the gradient rectangle
         p1 = (x1, y - 0.5 * height)
@@ -331,7 +331,7 @@ class ExonGlyph(BaseGlyph):
     """Multiple rectangles linked together."""
 
     def __init__(self, ax, x, y, mrnabed, exonbeds, height=0.03, ratio=1, align="left"):
-        super(ExonGlyph, self).__init__(ax)
+        super().__init__(ax)
         start, end = mrnabed.start, mrnabed.end
         xa = lambda a: x + (a - start) * ratio
         xb = lambda a: x - (end - a) * ratio
@@ -359,7 +359,7 @@ def __init__(
         shadow=False,
         **kwargs
     ):
-        super(GeneGlyph, self).__init__(ax)
+        super().__init__(ax)
         # Figure out the polygon vertices first
         orientation = 1 if x1 < x2 else -1
         level = 10
diff --git a/jcvi/graphics/karyotype.py b/jcvi/graphics/karyotype.py
index ae0e5726..1cbaa273 100644
--- a/jcvi/graphics/karyotype.py
+++ b/jcvi/graphics/karyotype.py
@@ -71,7 +71,7 @@ class Layout(AbstractLayout):
     def __init__(
         self, filename, delimiter=",", generank=False, seed: Optional[int] = None
     ):
-        super(Layout, self).__init__(filename)
+        super().__init__(filename)
         fp = open(filename)
         self.edges = []
         for row in fp:
diff --git a/jcvi/graphics/landscape.py b/jcvi/graphics/landscape.py
index 146c1034..bed4567e 100644
--- a/jcvi/graphics/landscape.py
+++ b/jcvi/graphics/landscape.py
@@ -70,7 +70,7 @@ def subtract(self, o):
 
 class BinFile(LineFile):
     def __init__(self, filename):
-        super(BinFile, self).__init__(filename)
+        super().__init__(filename)
         self.mapping = defaultdict(list)
 
         fp = open(filename, encoding="utf-8")
@@ -95,7 +95,7 @@ def __init__(self, row, delimiter=","):
 
 class ChrInfoFile(BaseFile, OrderedDict):
     def __init__(self, filename, delimiter=","):
-        super(ChrInfoFile, self).__init__(filename)
+        super().__init__(filename)
         with open(filename, encoding="utf-8") as fp:
             for row in fp:
                 if row[0] == "#":
@@ -116,7 +116,7 @@ def __init__(self, row, delimiter=","):
 
 class TitleInfoFile(BaseFile, OrderedDict):
     def __init__(self, filename, delimiter=","):
-        super(TitleInfoFile, self).__init__(filename)
+        super().__init__(filename)
         with open(filename, encoding="utf-8") as fp:
             for row in fp:
                 if row[0] == "#":
diff --git a/jcvi/graphics/synteny.py b/jcvi/graphics/synteny.py
index 7f56e770..179d3560 100644
--- a/jcvi/graphics/synteny.py
+++ b/jcvi/graphics/synteny.py
@@ -99,7 +99,7 @@ class Layout(AbstractLayout):
     """
 
     def __init__(self, filename, delimiter=",", seed: Optional[int] = None):
-        super(Layout, self).__init__(filename)
+        super().__init__(filename)
         fp = open(filename, encoding="utf-8")
         self.edges = []
         for row in fp:
diff --git a/jcvi/graphics/table.py b/jcvi/graphics/table.py
index 4a18b597..73f9fc92 100644
--- a/jcvi/graphics/table.py
+++ b/jcvi/graphics/table.py
@@ -24,7 +24,7 @@
 
 class CsvTable(list):
     def __init__(self, csvfile="table.csv"):
-        super(CsvTable, self).__init__()
+        super().__init__()
         with open(csvfile) as csvfile:
             reader = csv.reader(csvfile, skipinitialspace=True)
             self.header = [markup(x) for x in next(reader)]
diff --git a/jcvi/graphics/tree.py b/jcvi/graphics/tree.py
index 0c408fd5..8d96dc77 100644
--- a/jcvi/graphics/tree.py
+++ b/jcvi/graphics/tree.py
@@ -37,7 +37,7 @@ def __init__(self, row, delimiter=","):
 
 class LeafInfoFile(LineFile):
     def __init__(self, filename, delimiter=","):
-        super(LeafInfoFile, self).__init__(filename)
+        super().__init__(filename)
         self.cache = {}
         with open(filename) as fp:
             for row in fp:
@@ -59,7 +59,7 @@ def __init__(self, row, delimiter=",", defaultcolor="#7fc97f"):
 
 class WGDInfoFile(LineFile):
     def __init__(self, filename, delimiter=","):
-        super(WGDInfoFile, self).__init__(filename)
+        super().__init__(filename)
         self.cache = defaultdict(list)
         with open(filename) as fp:
             for row in fp:
diff --git a/jcvi/projects/napus.py b/jcvi/projects/napus.py
index 14c7c9a5..8e767e6c 100644
--- a/jcvi/projects/napus.py
+++ b/jcvi/projects/napus.py
@@ -63,7 +63,7 @@ def __init__(self, row, delimiter=","):
 
 class F4ALayout(LineFile):
     def __init__(self, filename, delimiter=","):
-        super(F4ALayout, self).__init__(filename)
+        super().__init__(filename)
         fp = open(filename)
         self.edges = []
         for row in fp:
diff --git a/jcvi/projects/pineapple.py b/jcvi/projects/pineapple.py
index 6c06ac5b..b092a47d 100644
--- a/jcvi/projects/pineapple.py
+++ b/jcvi/projects/pineapple.py
@@ -31,7 +31,7 @@ def __init__(self, line):
 
 class RegionsFile(LineFile):
     def __init__(self, filename):
-        super(RegionsFile, self).__init__(filename)
+        super().__init__(filename)
         fp = open(filename)
         next(fp)
         for row in fp:
diff --git a/jcvi/utils/aws.py b/jcvi/utils/aws.py
index ae3bdae8..0546df50 100644
--- a/jcvi/utils/aws.py
+++ b/jcvi/utils/aws.py
@@ -39,7 +39,7 @@
 
 class InstanceSkeleton(BaseFile):
     def __init__(self, filename=datafile("instance.json")):
-        super(InstanceSkeleton, self).__init__(filename)
+        super().__init__(filename)
         self.spec = json.load(open(filename))
 
     @property
diff --git a/jcvi/utils/cbook.py b/jcvi/utils/cbook.py
index a2712ffb..e11b1591 100644
--- a/jcvi/utils/cbook.py
+++ b/jcvi/utils/cbook.py
@@ -85,7 +85,7 @@ def wrapper(*args, **kwargs):
 
 class Registry(defaultdict):
     def __init__(self, *args, **kwargs):
-        super(Registry, self).__init__(list, *args, **kwargs)
+        super().__init__(list, *args, **kwargs)
 
     def iter_tag(self, tag):
         for key, ts in self.items():
diff --git a/jcvi/variation/delly.py b/jcvi/variation/delly.py
index 71f3200d..a8f1b5e0 100644
--- a/jcvi/variation/delly.py
+++ b/jcvi/variation/delly.py
@@ -44,7 +44,7 @@ def bedline(self):
 
 class Delly(BaseFile):
     def __init__(self, filename):
-        super(Delly, self).__init__(filename)
+        super().__init__(filename)
 
     def __iter__(self):
         fp = must_open(self.filename)
diff --git a/jcvi/variation/str.py b/jcvi/variation/str.py
index b35fc65e..750df228 100644
--- a/jcvi/variation/str.py
+++ b/jcvi/variation/str.py
@@ -91,7 +91,7 @@
 
 class TREDsRepo(dict):
     def __init__(self, ref=REF):
-        super(TREDsRepo, self).__init__()
+        super().__init__()
         self.ref = ref
         df = pd.read_csv(REPO, index_col=0)
         self.names = []
@@ -269,7 +269,7 @@ def fix_counts(self, subseq):
 class STRFile(LineFile):
     def __init__(self, lobstr_home, db="hg38"):
         filename = op.join(lobstr_home, "{0}/index.info".format(db))
-        super(STRFile, self).__init__(filename)
+        super().__init__(filename)
         fp = open(filename)
         for row in fp:
             self.append(STRLine(row))
@@ -285,7 +285,7 @@ def register(self):
 
 class LobSTRvcf(dict):
     def __init__(self, columnidsfile="STR.ids"):
-        super(LobSTRvcf, self).__init__()
+        super().__init__()
         self.samplekey = None
         self.evidence = {}  # name: (supporting reads, stutter reads)
         if columnidsfile: