def test_get_rgb255_notmatch(self):
# assert not incorrect conversions
randidx = numpy.random.randint(0,high=len(self.valid_colors),size=len(self.valid_colors))
for i,(my_str,_) in zip(randidx,self.valid_colors):
if self.valid_colors[i][0].upper() != my_str.upper():
self.assertNotEqual(tuple(get_rgb255(my_str)),
self.valid_colors[i][0])
def test_get_rgb255_notmatch(self):
# assert not incorrect conversions
randidx = numpy.random.randint(0,
high=len(self.valid_colors),
size=len(self.valid_colors))
for i, (my_str, _) in zip(randidx, self.valid_colors):
if self.valid_colors[i][0].upper() != my_str.upper():
self.assertNotEqual(tuple(get_rgb255(my_str)),
self.valid_colors[i][0])
def main(argv=sys.argv[1:]):
"""Command-line program
Parameters
----------
argv : list, optional
A list of command-line arguments, which will be processed
as if the script were called from the command line if
:py:func:`main` is called directly.
Default: sys.argv[1:] (actually command-line arguments)
"""
ap = AlignmentParser()
bp = BaseParser()
parser = argparse.ArgumentParser(description=format_module_docstring(__doc__),
formatter_class=argparse.RawDescriptionHelpFormatter,
parents=[bp.get_parser(),ap.get_parser()])
parser.add_argument("-o","--out",dest="outbase",type=str,required=True,
metavar="FILENAME",
help="Base name for output files")
parser.add_argument("--window_size",default=100000,metavar="N",type=int,
help="Size of nucleotides to fetch at once for export. "+\
"Large values are faster but require more memory "+\
"(Default: 100000)")
track_opts = parser.add_argument_group(title="Browser track options")
track_opts.add_argument("--color",type=str,default=None,
help="An RGB hex string (`'#NNNNNN'`, `N` in `[0-9,A-F]`) specifying \
the track color.")
track_opts.add_argument("-t","--track_name",dest="track_name",type=str,
help="Name to give browser track",
default=None)
track_opts.add_argument("--output_format",choices=("bedgraph","variable_step"),
default="bedgraph",
help="Format of output file (Default: bedgraph)")
args = parser.parse_args(argv)
gnd = ap.get_genome_array_from_args(args,printer=printer)
bp.get_base_ops_from_args(args)
if args.track_name is None:
name = args.outbase
else:
name = args.track_name
if args.color is not None:
fw_color = rc_color = "%s,%s,%s" % tuple(get_rgb255(args.color))
else:
fw_color = rc_color = "0,0,0"
if args.output_format == "bedgraph":
outfn = gnd.to_bedgraph
elif args.output_format == "variable_step":
outfn = gnd.to_variable_step
track_fw = "%s_fw.wig" % args.outbase
track_rc = "%s_rc.wig" % args.outbase
with argsopener(track_fw,args,"w") as fw_out:
printer.write("Writing forward strand track to %s ..." % track_fw)
outfn(fw_out,"%s_fw" % name,"+",window_size=args.window_size,color=fw_color,
printer=printer)
fw_out.close()
with argsopener(track_rc,args,"w") as rc_out:
printer.write("Writing reverse strand track to %s ..." % track_rc)
outfn(rc_out,"%s_rc" % name,"-",window_size=args.window_size,color=rc_color,
printer=printer)
rc_out.close()
printer.write("Done!")
def test_get_rgb255_match(self):
# test correct conversions
for my_str, my_tup in self.valid_colors:
self.assertEqual(tuple(get_rgb255(my_str)), my_tup)
def test_get_rgb255_match(self):
# test correct conversions
for my_str, my_tup in self.valid_colors:
self.assertEqual(tuple(get_rgb255(my_str)),my_tup)