def main(argv=None):
"""script main.
parses command line options in sys.argv, unless *argv* is given.
"""
if argv == None: argv = sys.argv
parser = E.OptionParser(
version=
"%prog version: $Id: codonbias_weights2tsv.py 2781 2009-09-10 11:33:14Z andreas $"
)
parser.add_option("--methods",
dest="methods",
type="string",
help="methods to apply.")
parser.add_option("--is-frequencies",
dest="is_frequencies",
action="store_true",
help="data is frequencies (default: weights).")
parser.add_option("-s",
"--sort",
dest="sort",
type="choice",
choices=("percent-difference", "aa"),
help="sort order of output table.")
parser.add_option(
"-g",
"--global-sort",
dest="global_sort",
action="store_true",
help="globally sort results (otherwise: by species pair).")
parser.set_defaults( \
methods = "",
is_frequencies = False,
sort = "percent-difference",
global_sort= False,
)
(options, args) = E.Start(parser)
if options.methods:
options.methods = options.methods.split(",")
fields, table = CSV.ReadTable(sys.stdin)
## convert weights to floats
table = CSV.getConvertedTable(table, range(1, len(fields)))
for method in options.methods:
if method == "overview":
if options.is_frequencies:
WriteOverviewFrequencies(fields, table, options)
else:
WriteOverviewWeights(fields, table, options)
def main(argv=None):
"""script main.
parses command line options in sys.argv, unless *argv* is given.
"""
if argv is None:
argv = sys.argv
parser = E.OptionParser(
version="%prog version: $Id: codonbias_weights2tsv.py 2781 2009-09-10 11:33:14Z andreas $")
parser.add_option("--methods", dest="methods", type="string",
help="methods to apply.")
parser.add_option("--is-frequencies", dest="is_frequencies", action="store_true",
help="data is frequencies (default: weights).")
parser.add_option("-s", "--sort", dest="sort", type="choice",
choices=("percent-difference", "aa"),
help="sort order of output table.")
parser.add_option("-g", "--global-sort", dest="global_sort", action="store_true",
help="globally sort results (otherwise: by species pair).")
parser.set_defaults(
methods="",
is_frequencies=False,
sort="percent-difference",
global_sort=False,
)
(options, args) = E.Start(parser)
if options.methods:
options.methods = options.methods.split(",")
fields, table = CSV.ReadTable(sys.stdin)
# convert weights to floats
table = CSV.getConvertedTable(table, range(1, len(fields)))
for method in options.methods:
if method == "overview":
if options.is_frequencies:
WriteOverviewFrequencies(fields, table, options)
else:
WriteOverviewWeights(fields, table, options)
choices=("percent-difference", "aa"),
help="sort order of output table.")
parser.add_option( "-g", "--global-sort", dest="global_sort", action="store_true",
help="globally sort results (otherwise: by species pair).")
parser.set_defaults( \
methods = "",
is_frequencies = False,
sort = "percent-difference",
global_sort= False,
)
(options, args) = E.Start( parser )
if options.methods:
options.methods = options.methods.split(",")
fields, table = CSV.ReadTable(sys.stdin)
## convert weights to floats
table = CSV.getConvertedTable( table, range( 1, len(fields) ) )
for method in options.methods:
if method == "overview":
if options.is_frequencies:
WriteOverviewFrequencies( fields, table, options )
else:
WriteOverviewWeights( fields, table, options )
