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1 #!/usr/bin/env python
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2 """Create ROI overview report.
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3
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4 This report consists of plots of all metrics (y: metric, x: rank of value).
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5 Each plot is written out as a PNG file and we also create one output HTML file
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6 that shows all HTML files.
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7
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8 Plotting is done using the fine matplotlib.
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9 """
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10
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11 from __future__ import print_function
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12
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13 __author__ = 'Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>'
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14 __copyright__ = 'Copyring 2013, Freie Universitaet Berlin'
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15 __license__ = 'BSD 3-clause'
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16
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17
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18 import sys
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19 import os
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20 import os.path
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21 import argparse
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22
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23 import Cheetah.Template
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24 import matplotlib.pyplot as plt
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25
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26 import ngs_roi.io
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27 import ngs_roi.app
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28 import ngs_roi.argparse
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29
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30
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31 # The HTML template to use for generating the HTML page.
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32 REPORT_TPL = """
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33 <html>
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34 <head>
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35 <title>ROI Report</title>
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36 </head>
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37 <body>
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38 <h1>ROI Report</h1>
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39 <h2>Table of Contents</h2>
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40 <ul>
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41 #for figure in $figures
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42 <li><a href="#$figure.slug">$figure.title</a></li>
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43 #end for
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44 </ul>
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45 <h2>Plots</h2>
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46 #for figure in $figures
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47 <h3 id="$figure.slug">$figure.title</h3>
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48 <img src="$figure.file_name" title="$figure.title" />
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49 #end for
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50 </body>
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51 </html>
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52 """
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53
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54
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55 class ReportBuilder(ngs_roi.app.App):
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56 """This class is used for building the report."""
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57
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58 def __init__(self, args):
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59 self.args = args
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60 self.in_file = self.args.in_file
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61 self.out_file = self.args.out_file
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62 self.out_dir = self.args.out_dir
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63 self.prepareOutDir()
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64
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65 def plotAndWrite(self, file_name, numbers, ylabel):
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66 """Create plot of numbers and write as PNG.
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67
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68 :param file_name:path to write plot to as image
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69 :param numbers:list of numbers to plot
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70 :param ylabel:label for y axis
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71 """
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72 plt.figure()
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73 plt.plot(numbers)
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74 plt.ylabel(ylabel)
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75 plt.savefig(file_name)
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76
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77 def run(self):
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78 # Load ROI.
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79 print('Loading ROI...', file=sys.stderr)
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80 records = ngs_roi.io.load(self.in_file)
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81 keys = records[0].data_keys
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82 # Create ROI plots.
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83 print('Creating plots...', file=sys.stderr)
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84 METRICS = [('start position', 'start_pos', lambda x: x.start_pos),
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85 ('end position', 'end_pos', lambda x: x.end_pos),
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86 ('region length', 'region_length', lambda x: x.region_length),
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87 ('max count', 'max_count', lambda x: x.max_count)]
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88 def getData(i):
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89 def func(x):
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90 try:
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91 res = float(x.data[i])
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92 except ValueError:
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93 res = 0
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94 return res
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95 return func
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96 for i, key in enumerate(keys):
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97 slug = ''.join(x for x in key if x.isalnum())
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98 METRICS.append((key, slug, getData(i)))
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99 figure_infos = []
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100 for title, slug, func in METRICS:
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101 values = [func(x) for x in records]
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102 file_name = 'report_%s.png' % slug
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103 file_path = os.path.join(self.out_dir, file_name)
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104 self.plotAndWrite(file_path, sorted(values), title)
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105 figure_infos.append({'file_name': file_name, 'title': title, 'slug': slug})
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106 # Create report HTML.
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107 name_space = {'figures': figure_infos}
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108 t = Cheetah.Template.Template(REPORT_TPL, searchList=name_space)
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109 with open(os.path.join(self.out_dir, 'index.html'), 'wb') as f:
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110 f.write(str(t))
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111 with open(os.path.join(self.out_file), 'wb') as f:
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112 f.write(str(t))
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113
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114 def main():
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115 """Program entry point."""
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116
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117 parser = argparse.ArgumentParser(description='Create ROI report.')
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118
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119 ngs_roi.argparse.addFileArguments(parser)
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120 args = parser.parse_args()
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121 ngs_roi.argparse.applyFileDefaults(args)
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122
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123 report_builder = ReportBuilder(args)
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124 return report_builder.run()
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125
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126
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127 if __name__ == '__main__':
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128 sys.exit(main())
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