run black

jcvi/apps/align.py

@@ -216,9 +216,7 @@ def nucmer(args):
     from jcvi.formats.base import split
 
     p = OptionParser(nucmer.__doc__)
-    p.add_option(
-        "--chunks", type=int, help="Split both query and subject into chunks"
-    )
+    p.add_option("--chunks", type=int, help="Split both query and subject into chunks")
     p.set_params(prog="nucmer", params="-l 100 -c 500")
     p.set_cpus()
     opts, args = p.parse_args(args)

jcvi/apps/uclust.py

@@ -556,9 +556,7 @@ def consensus(args):
     errors according to error rate, calls consensus.
     """
     p = OptionParser(consensus.__doc__)
-    p.add_option(
-        "--ploidy", default=2, type=int, help="Number of haplotypes per locus"
-    )
+    p.add_option("--ploidy", default=2, type=int, help="Number of haplotypes per locus")
     add_consensus_options(p)
     p.set_verbose()
     opts, args = p.parse_args(args)

jcvi/assembly/allmaps.py

@@ -1395,12 +1395,8 @@ def path(args):
     )
     p.add_option("--seqid", help="Only run partition with this seqid")
     p.add_option("--partitions", help="Use predefined partitions of LGs")
-    p.add_option(
-        "--links", default=10, type=int, help="Only plot matchings more than"
-    )
-    p.add_option(
-        "--mincount", default=1, type=int, help="Minimum markers on a contig"
-    )
+    p.add_option("--links", default=10, type=int, help="Only plot matchings more than")
+    p.add_option("--mincount", default=1, type=int, help="Minimum markers on a contig")
     p.add_option(
         "--noplot",
         default=False,
@@ -1783,9 +1779,7 @@ def add_allmaps_plot_options(p):
         choices=distance_choices,
         help="Plot markers based on distance",
     )
-    p.add_option(
-        "--links", default=10, type=int, help="Only plot matchings more than"
-    )
+    p.add_option("--links", default=10, type=int, help="Only plot matchings more than")
     p.add_option(
         "--panels", default=False, action="store_true", help="Add panel labels A/B"
     )

jcvi/assembly/syntenypath.py

@@ -140,9 +140,7 @@ def bed(args):
         action="store_true",
         help="Switch reference and aligned map elements",
     )
-    p.add_option(
-        "--scale", type=float, help="Scale the aligned map distance by factor"
-    )
+    p.add_option("--scale", type=float, help="Scale the aligned map distance by factor")
     p.set_beds()
     p.set_outfile()
     opts, args = p.parse_args(args)

jcvi/compara/catalog.py

@@ -509,9 +509,7 @@ def omgprepare(args):
 
     p = OptionParser(omgprepare.__doc__)
     p.add_option("--norbh", action="store_true", help="Disable RBH hits")
-    p.add_option(
-        "--pctid", default=0, type=int, help="Percent id cutoff for RBH hits"
-    )
+    p.add_option("--pctid", default=0, type=int, help="Percent id cutoff for RBH hits")
     p.add_option("--cscore", default=90, type=int, help="C-score cutoff for RBH hits")
     p.set_stripnames()
     p.set_beds()

jcvi/compara/synteny.py

@@ -1454,9 +1454,7 @@ def mcscan(args):
     tandem cluster as one line, tab separated.
     """
     p = OptionParser(mcscan.__doc__)
-    p.add_option(
-        "--iter", default=100, type=int, help="Max number of chains to output"
-    )
+    p.add_option("--iter", default=100, type=int, help="Max number of chains to output")
     p.add_option(
         "--ascii",
         default=False,

jcvi/formats/base.py

@@ -785,9 +785,7 @@ def group(args):
 
     p = OptionParser(group.__doc__)
     p.set_sep()
-    p.add_option(
-        "--groupby", default=None, type=int, help="Default column to groupby"
-    )
+    p.add_option("--groupby", default=None, type=int, help="Default column to groupby")
     p.add_option(
         "--groupsep", default=",", help="Separator to join the grouped elements"
     )

jcvi/formats/bed.py

@@ -2440,9 +2440,7 @@ def flanking(args):
     p.add_option(
         "--coord", default=None, type=int, help="coordinate of the position in query."
     )
-    p.add_option(
-        "-n", default=10, type=int, help="number of flanking features to get"
-    )
+    p.add_option("-n", default=10, type=int, help="number of flanking features to get")
     p.add_option(
         "--side",
         default="both",

jcvi/formats/fasta.py

@@ -540,9 +540,7 @@ def qual(args):
     from jcvi.formats.sizes import Sizes
 
     p = OptionParser(qual.__doc__)
-    p.add_option(
-        "--qv", default=31, type=int, help="Dummy qv score for extended bases"
-    )
+    p.add_option("--qv", default=31, type=int, help="Dummy qv score for extended bases")
     p.set_outfile()
     opts, args = p.parse_args(args)
 

jcvi/graphics/grabseeds.py

@@ -297,9 +297,7 @@ def add_seeds_options(p, args):
     g2.add_option(
         "--maxsize", default=50, type=float, help="Max percentage of object to image"
     )
-    g2.add_option(
-        "--count", default=100, type=int, help="Report max number of objects"
-    )
+    g2.add_option("--count", default=100, type=int, help="Report max number of objects")
     g2.add_option(
         "--watershed",
         default=False,

jcvi/projects/str.py

@@ -2044,9 +2044,7 @@ def compare2(args):
     Compare performances of various variant callers on simulated STR datasets.
     """
     p = OptionParser(compare2.__doc__)
-    p.add_option(
-        "--maxinsert", default=300, type=int, help="Maximum number of repeats"
-    )
+    p.add_option("--maxinsert", default=300, type=int, help="Maximum number of repeats")
     add_simulate_options(p)
     opts, args, iopts = p.set_image_options(args, figsize="10x5")
 
@@ -2101,9 +2099,7 @@ def power(args):
     This compares the power of various evidence types.
     """
     p = OptionParser(power.__doc__)
-    p.add_option(
-        "--maxinsert", default=300, type=int, help="Maximum number of repeats"
-    )
+    p.add_option("--maxinsert", default=300, type=int, help="Maximum number of repeats")
     add_simulate_options(p)
     opts, args, iopts = p.set_image_options(args, figsize="10x10", format="png")
 
@@ -2200,9 +2196,7 @@ def tredparse(args):
     Adds coverage comparisons as panel C and D.
     """
     p = OptionParser(tredparse.__doc__)
-    p.add_option(
-        "--maxinsert", default=300, type=int, help="Maximum number of repeats"
-    )
+    p.add_option("--maxinsert", default=300, type=int, help="Maximum number of repeats")
     add_simulate_options(p)
     opts, args, iopts = p.set_image_options(args, figsize="10x10")