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import sys
import string
import json
import itertools as it
from operator import itemgetter
import collections
from argparse import ArgumentParser
def main():
args = get_args()
traces = collections.defaultdict(list)
chroms = collections.OrderedDict()
chroms["total"] = True
for f in args.input:
sample = f.replace(".mosdepth.global.dist.txt", "")
gen = (x.rstrip().split("\t") for x in open(f))
for chrom, data in it.groupby(gen, itemgetter(0)):
if chrom.startswith("GL"):
continue
if "Un" in chrom: continue
if "random" in chrom or "HLA" in chrom: continue
if chrom.endswith("alt"): continue
chroms[chrom] = True
xs, ys = [], []
v50 = 0
found = False
for _, x, y in data:
y = float(y)
if y < 0.01:
continue
if not found and y > 0.5:
v50 = x
found = True
print("{}\t{}\t{}\t{:.3f}".format(sample, chrom, x, y))
xs.append(float(x))
ys.append(y)
if len(xs) > 100:
xs = [x for i, x in enumerate(xs) if ys[i] > 0.02]
ys = [y for y in ys if y > 0.02]
if len(xs) > 100:
xs = xs[::2]
ys = ys[::2]
traces[chrom].append({
'x': [round(x, 3) for x in xs],
'y': [round(y, 3) for y in ys],
'mode': 'lines',
'name': sample + (" (%.1f)" % float(v50))
})
tmpl = """<html>
<head>
<script src="https://cdn.plot.ly/plotly-latest.min.js"></script>
<style>
div {
width: 800px;
height: 420px;
}
</style
</head>
<body>$plot_divs</div>
<script>
var layout = {
hovermode: 'closest',
xaxis: {title: 'Coverage'},
yaxis: {title: 'Proportion of bases at coverage', domain: [0, 1], dtick: 0.25},
showlegend: $showlegend,
autosize: true,
legend: {
x: 0.1,
y: 0.1
},
}
"""
footer = """
</script>
</body>
</html>"""
chr_tmpl = """
Plotly.newPlot('plot-div-$chrom', $data, layout, {displayModeBar: false, displaylogo: false, fillFrame: false, autosizeable: true});
"""
tmpl = string.Template(tmpl)
try:
with open(args.output, "w") as html:
divs = "\n".join("<{div}>{chrom}</{div}><div id='plot-div-{chrom}'></div><hr/>".format(
chrom=c, div="h2" if c == "total" else "b") for c in chroms)
html.write(tmpl.substitute(showlegend="true" if len(
sys.argv[1:]) < 20 else "false", plot_divs=divs))
for chrom in chroms:
html.write(string.Template(chr_tmpl).substitute(
chrom=chrom, data=json.dumps(traces[chrom])))
html.write(footer)
except FileNotFoundError:
sys.exit("ERROR: failed creating output file, does the path exist?")
def get_args():
parser = ArgumentParser(description="Creates html plots from mosdepth results.")
parser.add_argument("-o", "--output",
default="dist.html",
help="path and name of output file. Directories must exist.")
parser.add_argument("input",
nargs='+',
help="the dist file(s) to use for plotting")
return parser.parse_args()
if __name__ == '__main__':
main()
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