Mercurial > repos > holtgrewe > ngs_roi

#!/usr/bin/env python
"""Generation of detailed ROI reports with larger plots.

This report generation works for hundred of ROIs.
"""

import 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 >>sys.stderr, 'Loading ROI'
        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 >>sys.stderr, 'Writing plot %s' % file_name
            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 >>sys.stderr, 'Writing HTML file %s' % file_name

        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())
author	holtgrewe
date	Tue, 14 May 2013 04:52:22 -0400
parents	0ac4f6f3d984
children	170e48a55078