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1 #!/usr/bin/env python
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2 """ROI Table Generator
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3
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4 Generates a HTML page with a table of ROI record details. Besides showing the
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5 numeric ROI information, it also gives little roi plots in a column.
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6
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7 For the little ROI plots, it calls the program roi_plot_thumbnails that has to
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8 be in the PATH.
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9 """
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10
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11 __author__ = 'Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>'
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12 __copyright__ = 'Copyring 2013, Freie Universitaet Berlin'
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13 __license__ = 'BSD 3-clause'
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14
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15
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16 # TODO(holtgrew): Actually call roi_plot_thumbnails
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17 # TODO(holtgrew): from __future__ use print_function
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18
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19
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20 import argparse
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21 import math
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22 import os.path
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23 import sys
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24
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25 import Cheetah.Template
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26
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27 import ngs_roi.app
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28 import ngs_roi.argparse
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29 import ngs_roi.io
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30
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31
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32 # Main template.
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33 PAGE_TPL = """
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34 <html>
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35 <head><title>ROI Table</title></head>
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36 <body>
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37 <h1>ROI Table</h1>
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38 $table
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1
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39 <div><code>$args</code></div>
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0
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40 </body>
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41 </html>
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42 """
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43
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44 # Template for a table.
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45 TABLE_TPL = """
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46 <table border="1">
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47 <tr>
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48 <th>plot</th>
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49 <th>chr</th>
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50 <th>start</th>
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51 <th>end</th>
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52 <th>name</th>
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53 <th>length</th>
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54 <th>strand</th>
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55 <th>max_count</th>
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56 #for i, key in enumerate($data_keys)
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57 <th>$key</th>
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58 #end for
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59 </tr>
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60 #for id, roi in enumerate($records)
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61 <tr>
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62 <td><div style="width:${args.plot_width}; margin:2px; height:${args.plot_height+1}; background:url(thumbnail_${imgId($id)}.png) -${imgX($id)} -${imgY($id)};"></div></td>
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63 <td>$roi.ref</td>
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64 <td style="text-align:right;">$fmtPos($roi.start_pos + 1)</td>
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65 <td style="text-align:right;">$fmtPos($roi.end_pos)</td>
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66 <td><a href="$href($roi)">$roi.region_name</a></td>
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67 <td style="text-align:right;">$fmtPos($roi.region_length)</td>
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68 <td style="text-align:center;">$roi.strand</td>
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69 <td style="text-align:right;">$roi.max_count</td>
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70 #for i, key in enumerate($data_keys)
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71 <td>$roi.data[$i]</td>
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72 #end for
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73 </tr>
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74 #end for
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75 </table>
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76 """
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77
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78
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79 class RoiTable(object):
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80 """A table of ROI records with small plots."""
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81
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82 def __init__(self, args, keys, records, app):
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83 self.args = args
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84 self.keys = keys
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85 self.records = records
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86 self.app = app
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87
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88 def tplFuncs(self):
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89 def intWithCommas(x):
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90 if type(x) not in [type(0), type(0L)]:
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91 raise TypeError("Parameter must be an integer.")
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92 if x < 0:
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93 return '-' + intWithCommas(-x)
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94 result = ''
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95 while x >= 1000:
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96 x, r = divmod(x, 1000)
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97 result = ",%03d%s" % (r, result)
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98 return "%d%s" % (x, result)
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99
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100 def imgId(idx):
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101 """Image id from roi record id."""
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102 return idx / (self.args.num_rows * self.args.num_cols)
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103
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104 def imgX(idx):
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105 """x position in image from record id."""
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106 x = idx % self.args.num_cols
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107 res = x * self.args.plot_width
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108 if x > 0:
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109 res += (x - 1) * 2
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110 return res
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111
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112 def imgY(idx):
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113 """y position in image from record id."""
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114 y = idx / self.args.num_cols
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115 res = y * self.args.plot_height
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116 res += y * 2
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117 return res
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118
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119 return {'fmtPos': intWithCommas, 'imgId': imgId, 'imgX': imgX, 'imgY': imgY}
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120
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121 def render(self):
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122 """Returns string with rendered table."""
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123 vals = {'data_keys': self.keys, 'records': self.records, 'args': self.args,
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124 'href': lambda x:self.app.buildHref(x.ref, x.start_pos, x.end_pos)}
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125 vals.update(self.tplFuncs())
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126 t = Cheetah.Template.Template(TABLE_TPL, searchList=vals)
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127 return str(t)
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128
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129
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130 class TableApp(ngs_roi.app.App):
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131 def __init__(self, args):
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132 # Call parent's constructor and create output directory.
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133 ngs_roi.app.App.__init__(self, args)
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134 self.prepareOutDir()
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135
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136 def run(self):
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137 # Load ROI records.
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138 print >>sys.stderr, 'Loading ROI'
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139 records = ngs_roi.io.load(self.args.in_file, self.args.max_rois)
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140 keys = []
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141 if records:
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142 keys = records[0].data_keys
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143
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144 # Create plots.
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145 print >>sys.stderr, 'Creating plots...'
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146 runner = ngs_roi.app.PlotThumbnailsRunner(self.args)
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147 runner.run()
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148
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149 # Create table.
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150 print >>sys.stderr, 'Creating table...'
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151 self.createHtml(self.args.out_file, keys, records)
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152 return 0
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153
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154 def createHtml(self, file_name, keys, records):
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155 print >>sys.stderr, 'Writing %s' % self.args.out_file
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156 vals = {'table': RoiTable(self.args, keys, records, self).render()}
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157 t = Cheetah.Template.Template(PAGE_TPL, searchList=vals)
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158 with open(self.args.out_file, 'wb') as f:
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159 f.write(str(t))
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160
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161
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162 def main():
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163 parser = argparse.ArgumentParser(description='Plot ROI file.')
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164
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165 ngs_roi.argparse.addFileArguments(parser)
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166 ngs_roi.argparse.addPlotGridArguments(parser, default_plot_height=60,
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167 default_plot_width=90)
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168 ngs_roi.argparse.addLinkArguments(parser)
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169 args = parser.parse_args()
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170 ngs_roi.argparse.applyFileDefaults(args)
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171
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172 app = TableApp(args)
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173 return app.run()
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174
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175
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176 if __name__ == '__main__':
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177 sys.exit(main())
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