def histogram(args):
"""
%prog histogram *.gff
Plot gene statistics based on output of stats. For each gff file, look to
see if the metrics folder (i.e. Exon_Length) contains the data and plot
them.
"""
from jcvi.graphics.histogram import histogram_multiple
p = OptionParser(histogram.__doc__)
p.add_option("--bins", dest="bins", default=40, type="int",
help="number of bins to plot in the histogram [default: %default]")
opts, args = p.parse_args(args)
if len(args) < 1:
sys.exit(not p.print_help())
gff_files = args
# metrics = ("Exon_Length", "Intron_Length", "Gene_Length", "Exon_Count")
colors = ("red", "green", "blue", "black")
vmaxes = (1000, 1000, 4000, 20)
xlabels = ("bp", "bp", "bp", "number")
for metric, color, vmax, xlabel in zip(metrics, colors, vmaxes, xlabels):
logging.debug("Parsing files in `{0}`..".format(metric))
numberfiles = [op.join(metric, op.basename(x).split(".")[0] + ".txt") \
for x in gff_files]
histogram_multiple(numberfiles, 0, vmax, xlabel, metric,
bins=opts.bins, facet=True, fill=color,
prefix=metric + ".")
def histogram(args):
"""
%prog histogram *.gff
Plot gene statistics based on output of stats. For each gff file, look to
see if the metrics folder (i.e. Exon_Length) contains the data and plot
them.
"""
from jcvi.graphics.histogram import histogram_multiple
p = OptionParser(histogram.__doc__)
p.add_option("--bins", dest="bins", default=40, type="int",
help="number of bins to plot in the histogram [default: %default]")
opts, args = p.parse_args(args)
if len(args) < 1:
sys.exit(not p.print_help())
gff_files = args
# metrics = ("Exon_Length", "Intron_Length", "Gene_Length", "Exon_Count")
colors = ("red", "green", "blue", "black")
vmaxes = (1000, 1000, 4000, 20)
xlabels = ("bp", "bp", "bp", "number")
for metric, color, vmax, xlabel in zip(metrics, colors, vmaxes, xlabels):
logging.debug("Parsing files in `{0}`..".format(metric))
numberfiles = [op.join(metric, op.basename(x).split(".")[0] + ".txt") \
for x in gff_files]
histogram_multiple(numberfiles, 0, vmax, xlabel, metric,
bins=opts.bins, facet=True, fill=color,
prefix=metric + ".")