Mercurial > repos > holtgrewe > ngs_roi
diff roi_report.py @ 0:61d9bdb6d519 draft
Uploaded
| author | holtgrewe |
|---|---|
| date | Thu, 18 Apr 2013 08:03:38 -0400 |
| parents | |
| children | 170e48a55078 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/roi_report.py Thu Apr 18 08:03:38 2013 -0400 @@ -0,0 +1,128 @@ +#!/usr/bin/env python +"""Create ROI overview report. + +This report consists of plots of all metrics (y: metric, x: rank of value). +Each plot is written out as a PNG file and we also create one output HTML file +that shows all HTML files. + +Plotting is done using the fine matplotlib. +""" + +from __future__ import print_function + +__author__ = 'Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>' +__copyright__ = 'Copyring 2013, Freie Universitaet Berlin' +__license__ = 'BSD 3-clause' + + +import sys +import os +import os.path +import argparse + +import Cheetah.Template +import matplotlib.pyplot as plt + +import ngs_roi.io +import ngs_roi.app +import ngs_roi.argparse + + +# The HTML template to use for generating the HTML page. +REPORT_TPL = """ +<html> + <head> + <title>ROI Report</title> + </head> + <body> + <h1>ROI Report</h1> + <h2>Table of Contents</h2> + <ul> + #for figure in $figures + <li><a href="#$figure.slug">$figure.title</a></li> + #end for + </ul> + <h2>Plots</h2> + #for figure in $figures + <h3 id="$figure.slug">$figure.title</h3> + <img src="$figure.file_name" title="$figure.title" /> + #end for + </body> +</html> +""" + + +class ReportBuilder(ngs_roi.app.App): + """This class is used for building the report.""" + + def __init__(self, args): + self.args = args + self.in_file = self.args.in_file + self.out_file = self.args.out_file + self.out_dir = self.args.out_dir + self.prepareOutDir() + + def plotAndWrite(self, file_name, numbers, ylabel): + """Create plot of numbers and write as PNG. + + :param file_name:path to write plot to as image + :param numbers:list of numbers to plot + :param ylabel:label for y axis + """ + plt.figure() + plt.plot(numbers) + plt.ylabel(ylabel) + plt.savefig(file_name) + + def run(self): + # Load ROI. + print('Loading ROI...', file=sys.stderr) + records = ngs_roi.io.load(self.in_file) + keys = records[0].data_keys + # Create ROI plots. + print('Creating plots...', file=sys.stderr) + METRICS = [('start position', 'start_pos', lambda x: x.start_pos), + ('end position', 'end_pos', lambda x: x.end_pos), + ('region length', 'region_length', lambda x: x.region_length), + ('max count', 'max_count', lambda x: x.max_count)] + def getData(i): + def func(x): + try: + res = float(x.data[i]) + except ValueError: + res = 0 + return res + return func + for i, key in enumerate(keys): + slug = ''.join(x for x in key if x.isalnum()) + METRICS.append((key, slug, getData(i))) + figure_infos = [] + for title, slug, func in METRICS: + values = [func(x) for x in records] + file_name = 'report_%s.png' % slug + file_path = os.path.join(self.out_dir, file_name) + self.plotAndWrite(file_path, sorted(values), title) + figure_infos.append({'file_name': file_name, 'title': title, 'slug': slug}) + # Create report HTML. + name_space = {'figures': figure_infos} + t = Cheetah.Template.Template(REPORT_TPL, searchList=name_space) + with open(os.path.join(self.out_dir, 'index.html'), 'wb') as f: + f.write(str(t)) + with open(os.path.join(self.out_file), 'wb') as f: + f.write(str(t)) + +def main(): + """Program entry point.""" + + parser = argparse.ArgumentParser(description='Create ROI report.') + + ngs_roi.argparse.addFileArguments(parser) + args = parser.parse_args() + ngs_roi.argparse.applyFileDefaults(args) + + report_builder = ReportBuilder(args) + return report_builder.run() + + +if __name__ == '__main__': + sys.exit(main())