Replace super(Clsas, self) => super() (#672)

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)

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 = []
 

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):
         """

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))

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)

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()"""

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)

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)

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))

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()

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

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:

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()]

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] == "#":

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):

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 =>

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)

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):

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 = []

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:

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)

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

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():

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

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"

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"

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)

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):

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:

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