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1 #!/usr/bin/env python
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2 """Generation of detailed ROI reports with larger plots.
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3
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4 This report generation works for hundred of ROIs.
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5 """
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6
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5
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7 try:
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8 import argparse
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9 except ImportError:
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10 import argparse26 as argparse
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0
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11 import math
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12 import os.path
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13 import sys
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14
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15 import Cheetah.Template
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16 import matplotlib.pyplot as plt
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17
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1
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18 import ngs_roi.app
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19 import ngs_roi.argparse
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20 import ngs_roi.io
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0
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21
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22 PAGE_TPL = """
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23 <html>
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1
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24 <head>
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25 <title>ROI Table</title>
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26 <style type="text/css">
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27 div.plot
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28 {
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29 float: left;
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30 padding: 4px;
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31 margin: 2px;
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32 width: 420px;
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33 }
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34
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35 .plot h2 { margin-top: 3px; margin-bottom: 3px; text-align: center; }
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36 .plot img { display: block; margin: 0 auto; }
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37 </style>
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38 </head>
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39 <body>
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40 <h1>Detailed ROI Report</h1>
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1
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41
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42 #for i, roi in enumerate($records)
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43 <div class="plot">
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44 <h2>${roi.ref}:${roi.start_pos + 1}-${roi.end_pos+1}</h2>
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45 <a href="${href($roi)}" target="dead"><img src="plot_${i}.png" /></a>
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46 <p>
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47 <b>chr:start-end</b> <a href="${href($roi)}" target="dead">${roi.ref}:${roi.start_pos}-${roi.end_pos} ${roi.strand}</a>;
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48 <b>region name</b> ${roi.region_name};
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49 <b>region length</b> ${roi.region_length};
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50 </p>
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51 #if $roi.data
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52 <p>#for j, key in enumerate($data_keys)#<b>$key:</b> ${roi.data[$j]}; #end for#</p>
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53 #end if
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54 </div>
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55 #end for
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56 <iframe name="dead" height="0" width="0"></iframe>
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57 <div><code>$args</code></div>
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58 </body>
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59 </html>
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60 """
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61
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62 class DetailedRoiGenerator(ngs_roi.app.App):
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63 """Generate detailed ROI report.
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64
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65 :ivar args:Arguments from the comment line.
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66 """
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67
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68 def __init__(self, args):
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69 self.args = args
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70
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71 def run(self):
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72 """Run report generation, return status code.
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73
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74 :return: integer with the result.
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75 """
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76 print >>sys.stderr, 'Loading ROI'
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1
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77 records = ngs_roi.io.load(self.args.in_file, self.args.max_rois)
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78 keys = records[0].data_keys
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79
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80 self.writeHtml(keys, records)
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81 self.writePlots(records)
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82 return 0
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83
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84 def writePlots(self, records):
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85 COLOR = 'blue'
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86 LINE_WIDTH = .5
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87 LINE_STYLE = '-'
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88 TICK_FONT_SIZE = 8
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89 LABEL_FONT_SIZE = 10
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90 for i, roi in enumerate(records):
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91 file_name = 'plot_%d.png' % i
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92 file_name = os.path.join(self.args.out_dir, file_name)
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93 print >>sys.stderr, 'Writing plot %s' % file_name
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94 plt.figure(figsize=(4, 2.5))
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95 plt.gcf().subplots_adjust(bottom=0.16, left=0.15)
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96 plt.plot(roi.points, color=COLOR, linewidth=LINE_WIDTH, linestyle=LINE_STYLE)
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97 plt.ylim(ymin=0)
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98 if self.args.max_value:
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99 plt.ylim(ymax=self.args.max_value)
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100 plt.tick_params(labelsize=TICK_FONT_SIZE)
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101 plt.ylabel('coverage', fontsize=LABEL_FONT_SIZE, weight='semibold')
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102 plt.xlabel('ROI beginPos', fontsize=LABEL_FONT_SIZE, weight='semibold')
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103 plt.savefig(file_name)
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104
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105 def writeHtml(self, keys, records):
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106 file_name = self.args.out_file
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107 print >>sys.stderr, 'Writing HTML file %s' % file_name
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108
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109 vals = {'args': self.args, 'records': records, 'data_keys': keys,
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110 'href': lambda x: self.buildHref(x.ref, x.start_pos, x.end_pos)}
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111 t = Cheetah.Template.Template(PAGE_TPL, searchList=vals)
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112
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113 with open(file_name, 'wb') as f:
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114 f.write(str(t))
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115
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116
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117 def main():
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118 parser = argparse.ArgumentParser(description='Plot ROI file.')
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119 ngs_roi.argparse.addFileArguments(parser)
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120 ngs_roi.argparse.addPlotGridArguments(parser)
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121 ngs_roi.argparse.addLinkArguments(parser)
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122 args = parser.parse_args()
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123 ngs_roi.argparse.applyFileDefaults(args)
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124
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125 app = DetailedRoiGenerator(args)
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126 return app.run()
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127
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128
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129 if __name__ == '__main__':
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130 sys.exit(main())
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