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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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5
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20 try:
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21 import argparse
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22 except ImportError:
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23 import argparse26 as argparse
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0
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24 import math
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25 import os.path
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26 import sys
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27
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28 import Cheetah.Template
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29
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30 import ngs_roi.app
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31 import ngs_roi.argparse
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32 import ngs_roi.io
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33
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34
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35 # Main template.
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36 PAGE_TPL = """
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37 <html>
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38 <head><title>ROI Table</title></head>
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39 <body>
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40 <h1>ROI Table</h1>
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41 $table
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1
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42 <div><code>$args</code></div>
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0
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43 </body>
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44 </html>
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45 """
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46
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47 # Template for a table.
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48 TABLE_TPL = """
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49 <table border="1">
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50 <tr>
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51 <th>plot</th>
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52 <th>chr</th>
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53 <th>start</th>
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54 <th>end</th>
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55 <th>name</th>
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56 <th>length</th>
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57 <th>strand</th>
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58 <th>max_count</th>
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59 #for i, key in enumerate($data_keys)
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60 <th>$key</th>
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61 #end for
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62 </tr>
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63 #for id, roi in enumerate($records)
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64 <tr>
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65 <td><div style="width:${args.plot_width}; margin:2px; height:${args.plot_height+1}; background:url(thumbnail_${imgId($id)}.png) -${imgX($id)} -${imgY($id)};"></div></td>
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66 <td>$roi.ref</td>
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67 <td style="text-align:right;">$fmtPos($roi.start_pos + 1)</td>
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68 <td style="text-align:right;">$fmtPos($roi.end_pos)</td>
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69 <td><a href="$href($roi)">$roi.region_name</a></td>
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70 <td style="text-align:right;">$fmtPos($roi.region_length)</td>
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71 <td style="text-align:center;">$roi.strand</td>
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72 <td style="text-align:right;">$roi.max_count</td>
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73 #for i, key in enumerate($data_keys)
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74 <td>$roi.data[$i]</td>
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75 #end for
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76 </tr>
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77 #end for
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78 </table>
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79 """
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80
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81
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82 class RoiTable(object):
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83 """A table of ROI records with small plots."""
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84
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85 def __init__(self, args, keys, records, app):
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86 self.args = args
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87 self.keys = keys
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88 self.records = records
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89 self.app = app
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90
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91 def tplFuncs(self):
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92 def intWithCommas(x):
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93 if type(x) not in [type(0), type(0L)]:
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94 raise TypeError("Parameter must be an integer.")
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95 if x < 0:
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96 return '-' + intWithCommas(-x)
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97 result = ''
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98 while x >= 1000:
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99 x, r = divmod(x, 1000)
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100 result = ",%03d%s" % (r, result)
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101 return "%d%s" % (x, result)
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102
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103 def imgId(idx):
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104 """Image id from roi record id."""
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105 return idx / (self.args.num_rows * self.args.num_cols)
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106
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107 def imgX(idx):
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108 """x position in image from record id."""
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109 x = idx % self.args.num_cols
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110 res = x * self.args.plot_width
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111 if x > 0:
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112 res += (x - 1) * 2
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113 return res
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114
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115 def imgY(idx):
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116 """y position in image from record id."""
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117 y = idx / self.args.num_cols
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118 res = y * self.args.plot_height
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119 res += y * 2
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120 return res
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121
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122 return {'fmtPos': intWithCommas, 'imgId': imgId, 'imgX': imgX, 'imgY': imgY}
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123
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124 def render(self):
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125 """Returns string with rendered table."""
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126 vals = {'data_keys': self.keys, 'records': self.records, 'args': self.args,
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127 'href': lambda x:self.app.buildHref(x.ref, x.start_pos, x.end_pos)}
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128 vals.update(self.tplFuncs())
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129 t = Cheetah.Template.Template(TABLE_TPL, searchList=vals)
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130 return str(t)
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131
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132
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133 class TableApp(ngs_roi.app.App):
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134 def __init__(self, args):
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135 # Call parent's constructor and create output directory.
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136 ngs_roi.app.App.__init__(self, args)
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137 self.prepareOutDir()
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138
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139 def run(self):
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140 # Load ROI records.
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141 print >>sys.stderr, 'Loading ROI'
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142 records = ngs_roi.io.load(self.args.in_file, self.args.max_rois)
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143 keys = []
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144 if records:
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145 keys = records[0].data_keys
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146
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147 # Create plots.
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148 print >>sys.stderr, 'Creating plots...'
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149 runner = ngs_roi.app.PlotThumbnailsRunner(self.args)
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150 runner.run()
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151
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152 # Create table.
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153 print >>sys.stderr, 'Creating table...'
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154 self.createHtml(self.args.out_file, keys, records)
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155 return 0
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156
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157 def createHtml(self, file_name, keys, records):
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158 print >>sys.stderr, 'Writing %s' % self.args.out_file
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159 vals = {'table': RoiTable(self.args, keys, records, self).render(),
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160 'args': self.args}
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161 t = Cheetah.Template.Template(PAGE_TPL, searchList=vals)
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162 with open(self.args.out_file, 'wb') as f:
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163 f.write(str(t))
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164
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165
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166 def main():
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167 parser = argparse.ArgumentParser(description='Plot ROI file.')
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168
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169 ngs_roi.argparse.addFileArguments(parser)
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170 ngs_roi.argparse.addPlotGridArguments(parser, default_plot_height=60,
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171 default_plot_width=90)
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172 ngs_roi.argparse.addLinkArguments(parser)
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173 args = parser.parse_args()
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174 ngs_roi.argparse.applyFileDefaults(args)
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175
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176 app = TableApp(args)
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177 return app.run()
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178
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179
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180 if __name__ == '__main__':
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181 sys.exit(main())
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