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#!/usr/bin/env python3
"""Generation of detailed ROI reports with larger plots.
This report generation works for hundred of ROIs.
"""
try:
import argparse
except ImportError:
import argparse26 as argparse
import math
import os.path
import sys
import Cheetah.Template
import matplotlib.pyplot as plt
import ngs_roi.app
import ngs_roi.argparse
import ngs_roi.io
PAGE_TPL = """
<html>
<head>
<title>ROI Table</title>
<style type="text/css">
div.plot
{
float: left;
padding: 4px;
margin: 2px;
width: 420px;
}
.plot h2 { margin-top: 3px; margin-bottom: 3px; text-align: center; }
.plot img { display: block; margin: 0 auto; }
</style>
</head>
<body>
<h1>Detailed ROI Report</h1>
#for i, roi in enumerate($records)
<div class="plot">
<h2>${roi.ref}:${roi.start_pos + 1}-${roi.end_pos+1}</h2>
<a href="${href($roi)}" target="dead"><img src="plot_${i}.png" /></a>
<p>
<b>chr:start-end</b> <a href="${href($roi)}" target="dead">${roi.ref}:${roi.start_pos}-${roi.end_pos} ${roi.strand}</a>;
<b>region name</b> ${roi.region_name};
<b>region length</b> ${roi.region_length};
</p>
#if $roi.data
<p>#for j, key in enumerate($data_keys)#<b>$key:</b> ${roi.data[$j]}; #end for#</p>
#end if
</div>
#end for
<iframe name="dead" height="0" width="0"></iframe>
<div><code>$args</code></div>
</body>
</html>
"""
class DetailedRoiGenerator(ngs_roi.app.App):
"""Generate detailed ROI report.
:ivar args:Arguments from the comment line.
"""
def __init__(self, args):
self.args = args
def run(self):
"""Run report generation, return status code.
:return: integer with the result.
"""
print('Loading ROI', file=sys.stderr)
records = ngs_roi.io.load(self.args.in_file, self.args.max_rois)
keys = records[0].data_keys
self.writeHtml(keys, records)
self.writePlots(records)
return 0
def writePlots(self, records):
COLOR = 'blue'
LINE_WIDTH = .5
LINE_STYLE = '-'
TICK_FONT_SIZE = 8
LABEL_FONT_SIZE = 10
for i, roi in enumerate(records):
file_name = 'plot_%d.png' % i
file_name = os.path.join(self.args.out_dir, file_name)
print('Writing plot %s' % file_name, file=sys.stderr)
plt.figure(figsize=(4, 2.5))
plt.gcf().subplots_adjust(bottom=0.16, left=0.15)
plt.plot(roi.points, color=COLOR, linewidth=LINE_WIDTH, linestyle=LINE_STYLE)
plt.ylim(ymin=0)
if self.args.max_value:
plt.ylim(ymax=self.args.max_value)
plt.tick_params(labelsize=TICK_FONT_SIZE)
plt.ylabel('coverage', fontsize=LABEL_FONT_SIZE, weight='semibold')
plt.xlabel('ROI beginPos', fontsize=LABEL_FONT_SIZE, weight='semibold')
plt.savefig(file_name)
def writeHtml(self, keys, records):
file_name = self.args.out_file
print('Writing HTML file %s' % file_name, file=sys.stderr)
vals = {'args': self.args, 'records': records, 'data_keys': keys,
'href': lambda x: self.buildHref(x.ref, x.start_pos, x.end_pos)}
t = Cheetah.Template.Template(PAGE_TPL, searchList=vals)
with open(file_name, 'wb') as f:
f.write(str(t))
def main():
parser = argparse.ArgumentParser(description='Plot ROI file.')
ngs_roi.argparse.addFileArguments(parser)
ngs_roi.argparse.addPlotGridArguments(parser)
ngs_roi.argparse.addLinkArguments(parser)
args = parser.parse_args()
ngs_roi.argparse.applyFileDefaults(args)
app = DetailedRoiGenerator(args)
return app.run()
if __name__ == '__main__':
sys.exit(main())
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