def info():
from bioconvert.core.registry import Registry
r = Registry()
info = r.get_info()
converters = [x for x in info.items()]
data = [info[k] for k,v in info.items()]
msg = "Bioconvert contains {} converters including {} methods"
return msg.format(len(converters), sum(data))
def main(args=None):
if args is None:
args = sys.argv[1:]
arg_parser = argparse.ArgumentParser(
prog="bioconvert",
description="""Convertor infer the
formats from the first command. We do
not scan the input file. Therefore
users must ensure that their input
format files are properly
formatted.""",
formatter_class=argparse.RawDescriptionHelpFormatter,
epilog="""
Please visit http://bioconvert.readthedocs.org for more information about the
project or formats available.
Bioconvert is an open source collaborative project. Please feel free to
join us at https://github/biokit/bioconvert
""")
arg_parser.add_argument(
"-v",
"--verbosity",
default=bioconvert.logger.level,
help="Set the outpout verbosity.",
choices=["DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"],
)
arg_parser.add_argument("--no-plot", action="store_true")
args = arg_parser.parse_args(args)
from bioconvert.core.registry import Registry
r = Registry()
info = r.get_info()
# The available unique converters
converters = [x for x in info.items()]
# the number of methods per converter
data = [info[k] for k, v in info.items()]
# the number of formats
A1 = [x[0] for x in list(r.get_conversions())]
A2 = [x[1] for x in list(r.get_conversions())]
formats = set(A1 + A2)
print("Number of formats: {}".format(len(formats)))
print("Number of converters: {}".format(len(converters)))
print("Number of methods : {}".format(sum(data)))
if args.no_plot is False:
from pylab import hist, clf, xlabel, grid, show
clf()
hist(data, range(17), ec="k", zorder=2, align="left")
xlabel("Number of methods")
grid(zorder=-1)
show()
# If not, see <http://www.gnu.org/licenses/>. #
###########################################################################
"""
Available methods per converter
=====================================
Plot number of implemented methods per converter.
"""
#################################################
#
from bioconvert.core.registry import Registry
r = Registry()
info = r.get_info()
# The available unique converters
converters = [x for x in info.items()]
# the number of methods per converter
data = [info[k] for k, v in info.items()]
# the number of formats
A1 = [x[0] for x in list(r.get_conversions())]
A2 = [x[1] for x in list(r.get_conversions())]
formats = set(A1 + A2)
print("Number of formats: {}".format(len(formats)))
print("Number of converters: {}".format(len(converters)))
print("Number of methods : {}".format(sum(data)))
# create the sphinx code to include all converters
# author: Thomas Cokelaer 2018
from bioconvert.core.registry import Registry
reg = Registry()
convs = list(reg.get_info())
names = sorted([l.__module__ for l in convs])
def underline(text, character="-"):
return text + "\n" + character * len(text) + "\n"
print(underline("Reference converters", "="))
print(underline("Summary", "-"))
print(".. autosummary::\n")
for name in names:
print("\t{}".format(name))
print(underline("All converters documentation", "-"))
print()
for name in names:
print("""
.. automodule:: {}
:members:
:synopsis:
:private-members:""".format(name))
