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#!/usr/bin/env python3
"""ROI Table Generator
Generates a HTML page with a table of ROI record details. Besides showing the
numeric ROI information, it also gives little roi plots in a column.
For the little ROI plots, it calls the program roi_plot_thumbnails that has to
be in the PATH.
"""
__author__ = 'Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>'
__copyright__ = 'Copyring 2013, Freie Universitaet Berlin'
__license__ = 'BSD 3-clause'
# TODO(holtgrew): Actually call roi_plot_thumbnails
# TODO(holtgrew): from __future__ use print_function
try:
import argparse
except ImportError:
import argparse26 as argparse
import math
import os.path
import sys
import Cheetah.Template
import ngs_roi.app
import ngs_roi.argparse
import ngs_roi.io
# Main template.
PAGE_TPL = """
<html>
<head><title>ROI Table</title></head>
<body>
<h1>ROI Table</h1>
$table
<div><code>$args</code></div>
</body>
</html>
"""
# Template for a table.
TABLE_TPL = """
<table border="1">
<tr>
<th>plot</th>
<th>chr</th>
<th>start</th>
<th>end</th>
<th>name</th>
<th>length</th>
<th>strand</th>
<th>max_count</th>
#for i, key in enumerate($data_keys)
<th>$key</th>
#end for
</tr>
#for id, roi in enumerate($records)
<tr>
<td><div style="width:${args.plot_width}; margin:2px; height:${args.plot_height+1}; background:url(thumbnail_${imgId($id)}.png) -${imgX($id)} -${imgY($id)};"></div></td>
<td>$roi.ref</td>
<td style="text-align:right;">$fmtPos($roi.start_pos + 1)</td>
<td style="text-align:right;">$fmtPos($roi.end_pos)</td>
<td><a href="$href($roi)">$roi.region_name</a></td>
<td style="text-align:right;">$fmtPos($roi.region_length)</td>
<td style="text-align:center;">$roi.strand</td>
<td style="text-align:right;">$roi.max_count</td>
#for i, key in enumerate($data_keys)
<td>$roi.data[$i]</td>
#end for
</tr>
#end for
</table>
"""
class RoiTable(object):
"""A table of ROI records with small plots."""
def __init__(self, args, keys, records, app):
self.args = args
self.keys = keys
self.records = records
self.app = app
def tplFuncs(self):
def intWithCommas(x):
if type(x) not in [type(0), type(0)]:
raise TypeError("Parameter must be an integer.")
if x < 0:
return '-' + intWithCommas(-x)
result = ''
while x >= 1000:
x, r = divmod(x, 1000)
result = ",%03d%s" % (r, result)
return "%d%s" % (x, result)
def imgId(idx):
"""Image id from roi record id."""
return idx / (self.args.num_rows * self.args.num_cols)
def imgX(idx):
"""x position in image from record id."""
x = idx % self.args.num_cols
res = x * self.args.plot_width
if x > 0:
res += (x - 1) * 2
return res
def imgY(idx):
"""y position in image from record id."""
y = idx / self.args.num_cols
res = y * self.args.plot_height
res += y * 2
return res
return {'fmtPos': intWithCommas, 'imgId': imgId, 'imgX': imgX, 'imgY': imgY}
def render(self):
"""Returns string with rendered table."""
vals = {'data_keys': self.keys, 'records': self.records, 'args': self.args,
'href': lambda x:self.app.buildHref(x.ref, x.start_pos, x.end_pos)}
vals.update(self.tplFuncs())
t = Cheetah.Template.Template(TABLE_TPL, searchList=vals)
return str(t)
class TableApp(ngs_roi.app.App):
def __init__(self, args):
# Call parent's constructor and create output directory.
ngs_roi.app.App.__init__(self, args)
self.prepareOutDir()
def run(self):
# Load ROI records.
print('Loading ROI', file=sys.stderr)
records = ngs_roi.io.load(self.args.in_file, self.args.max_rois)
keys = []
if records:
keys = records[0].data_keys
# Create plots.
print('Creating plots...', file=sys.stderr)
runner = ngs_roi.app.PlotThumbnailsRunner(self.args)
runner.run()
# Create table.
print('Creating table...', file=sys.stderr)
self.createHtml(self.args.out_file, keys, records)
return 0
def createHtml(self, file_name, keys, records):
print('Writing %s' % self.args.out_file, file=sys.stderr)
vals = {'table': RoiTable(self.args, keys, records, self).render(),
'args': self.args}
t = Cheetah.Template.Template(PAGE_TPL, searchList=vals)
with open(self.args.out_file, '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, default_plot_height=60,
default_plot_width=90)
ngs_roi.argparse.addLinkArguments(parser)
args = parser.parse_args()
ngs_roi.argparse.applyFileDefaults(args)
app = TableApp(args)
return app.run()
if __name__ == '__main__':
sys.exit(main())
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