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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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7 import argparse
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8 import math
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9 import os.path
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10 import sys
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11
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12 import Cheetah.Template
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13 import matplotlib.pyplot as plt
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14
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15 import rois
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16
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17 PAGE_TPL = """
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18 <html>
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19 <head><title>ROI Table</title></head>
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20 <body>
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21 <h1>Detailed ROI Report</h1>
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22 #for i, roi in enumerate($records)
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23 <h2>${roi.ref}:${roi.start_pos + 1}-${roi.end_pos+1}</h2>
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24 <img src="${args.out_prefix}${i}.png" />
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25 <dl>
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26 <dt>chr:start-end name length strand</dt>
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27 <dd>${roi.ref}:${roi.start_pos}-${roi.end_pos} ${roi.region_name} ${roi.region_length} ${roi.strand}</dd>
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28 <dt>metrics</dt>
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29 <dd>#for j, key in enumerate($data_keys)#$key: ${roi.data[$j]}, #end for#</dd>
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30 </dl>
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31 #end for
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32 </body>
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33 </html>
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34 """
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35
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36 class DetailedRoiGenerator(object):
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37 """Generate detailed ROI report.
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38
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39 :ivar args:Arguments from the comment line.
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40 """
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41
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42 def __init__(self, args):
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43 self.args = args
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44
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45 def run(self):
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46 """Run report generation, return status code.
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47
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48 :return: integer with the result.
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49 """
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50 print >>sys.stderr, 'Loading ROI'
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51 keys, records = rois.loadRoi(self.args.in_file, self.args.max_rois)
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52
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53 self.writeHtml(keys, records)
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54 self.writePlots(records)
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55 return 0
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56
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57 def writePlots(self, records):
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58 for i, roi in enumerate(records):
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59 file_name = '%s%d.png' % (os.path.join(self.args.out_dir, self.args.out_prefix), i)
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60 print >>sys.stderr, 'Writing plot %s' % file_name
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61 plt.figure(figsize=(6, 4))
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62 plt.gcf().subplots_adjust(bottom=0.1, left=0.1)
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63 plt.plot(roi.points)
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64 plt.ylabel('coverage')
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65 plt.xlabel('ROI pos')
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66 plt.savefig(file_name)
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67
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68 def writeHtml(self, keys, records):
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69 file_name = self.args.out_file
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70 print >>sys.stderr, 'Writing HTML file %s' % file_name
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71
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72 vals = {'args': self.args, 'records': records, 'data_keys': keys}
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73 t = Cheetah.Template.Template(PAGE_TPL, searchList=vals)
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74
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75 with open(file_name, 'wb') as f:
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76 f.write(str(t))
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77
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78
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79 def main():
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80 parser = argparse.ArgumentParser(description='Plot ROI file.')
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81 parser.add_argument('-o', '--out-file', dest='out_file', metavar='PATH',
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82 help='Prefix of output HTML file. The tool will create '
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83 'PNG files parallel to the HTML file.',
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84 default='roi_plots.html')
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85 parser.add_argument('-d', '--out-dir', dest='out_dir', metavar='DIR',
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86 help='Directory to write images to. By default '
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87 'this is the same as the directory for --out-file.',
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88 default=None)
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89 parser.add_argument('-p', '--out-prefix', dest='out_prefix', metavar='DIR',
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90 help='Prefix of output PNG files.', default='roi_plot_grid')
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91 parser.add_argument('-i', '--in-file', dest='in_file', metavar='FILE',
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92 required=True, help='Path to ROI file to read.')
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93
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94 group = parser.add_argument_group('Plot Configuration', 'Arguments for the plot images.')
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95
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96 group.add_argument('--max-rois', dest='max_rois', metavar='NUM',
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97 type=int, default=0,
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98 help='Maximal number of ROIs, 0 for all.')
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99
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100 group.add_argument('--num-rows', dest='num_rows', metavar='ROWS',
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101 type=int, default=50,
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102 help='Number of rows per grid.')
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103 group.add_argument('--num-cols', dest='num_cols', metavar='COLS',
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104 type=int, default=40,
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105 help='Number of columns per grid.')
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106
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107 group.add_argument('--plot-height', dest='plot_height', metavar='HEIGHT',
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108 type=int, default=30, help='Height of one plot in px.')
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109 group.add_argument('--plot-width', dest='plot_width', metavar='WIDTH',
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110 type=int, default=30, help='Width of one plot in px.')
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111
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112 group = parser.add_argument_group('HTML Links', 'Arguments for HTML link creation.')
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113
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114 group.add_argument('--link-target', dest='link_target', metavar='TARGET',
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115 default='_blank', choices=['_blank', '_top'],
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116 help='Select the link target to create (_blank or _top).')
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117
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118 group.add_argument('--link-type', dest='link_type', metavar='TARGET',
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119 default='local_igv', choices=['local_igv', 'ucsc'],
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120 help='Select the type of links to create. One of '
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121 '"local_igv" and "ucsc".')
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122
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123 group.add_argument('--igv-host', dest='igv_host', metavar='HOST',
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124 default='localhost', help='Host for IGV link.')
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125 group.add_argument('--igv-port', dest='igv_port', metavar='PORT',
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126 type=int, default='60151', help='Port for IGV link.')
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127
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128 group.add_argument('--ucsc-org', dest='ucsc_org', metavar='ORG',
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129 default='human', help='Organism for UCSC browser link.')
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130 group.add_argument('--ucsc-db', dest='ucsc_db', metavar='DB',
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131 default='hg18', help='Assembly version for UCSC browser link.')
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132 group.add_argument('--ucsc-chr-prefix', dest='ucsc_chr_prefix', metavar='PREFIX',
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133 default='', help='Prefix for chromosome names in UCSC browser.')
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134
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135 args = parser.parse_args()
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136 if not args.out_dir:
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137 args.out_dir = os.path.dirname(args.out_file) or '.'
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138 print args
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139 app = DetailedRoiGenerator(args)
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140 return app.run()
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141
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142
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143 if __name__ == '__main__':
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144 sys.exit(main())
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