#!/usr/bin/env python3 """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. """ __author__ = 'Manuel Holtgrewe ' __copyright__ = 'Copyring 2013, Freie Universitaet Berlin' __license__ = 'BSD 3-clause' import sys import os import os.path try: import argparse except ImportError: import argparse26 as 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 = """ ROI Report

ROI Report

$figure.title

Plots

#for figure in $figures

$figure.title

#end for """ 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())

ROI Report

Table of Contents

Plots

$figure.title