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1 #!/usr/bin/env python
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2 """Thumbnail Plot Generator.
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3
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4 This report generator uses the binary roi_plot_thumbnails (C++ program, must
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5 be in PATH) to generate many PNG images with small ROI plots. It then creates
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6 a HTML file that includes the PNG and adds an overlay image link map such that
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7 when the user clicks on a plot, she is transfered to the according position in
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8 a local IGV or the UCSC genome browser, for example.
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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 # TODO(holtgrew): Use Cheetah templates to generate HTML.
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16 # TODO(holtgrew): Call roi_plot_thumbnails from Python script.
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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 ngs_roi.app
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26 import ngs_roi.argparse
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27 import ngs_roi.io
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28
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29
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30 class LinkRegion(object):
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31 """Region on picture with genomic interval."""
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32
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33 def __init__(self, x1, y1, x2, y2, ref, begin_pos, end_pos):
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34 self.x1 = x1
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35 self.x2 = x2
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36 self.y1 = y1
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37 self.y2 = y2
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38 self.ref = ref
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39 self.begin_pos = begin_pos
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40 self.end_pos = end_pos
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41
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42
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43 class RoiPlotGrid(object):
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44 """A grid of ROI plots.
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45
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46 width -- width one one plot
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47 height -- height of one plot
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48 """
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49
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50 # Border in each direction.
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51 BORDER = 0
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52 # Spacing between plots.
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53 SPACE = 2
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54
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55 def __init__(self, width, height, columns, rows, bg_plot=(0, 0, 0, 10),
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56 frame_col=(80, 80, 80, 255), fg_col=(0, 0, 0, 255)):
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57 # Properties of the grid.
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58 self.width = float(width)
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59 self.height = float(height)
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60 self.columns = columns
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61 self.rows = rows
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62 # State.
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63 self.idx = 0 # currently drawn plot
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64 self.canvas_width = 2 * self.BORDER + columns * width + (columns - 1) * self.SPACE
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65 self.canvas_height = 2 * self.BORDER + rows * height + (rows - 1) * self.SPACE
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66 # Colors.
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67 self.bg_plot = bg_plot
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68 self.frame_col = frame_col
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69 self.fg_color = fg_col
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70 # List of link region for image map.
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71 self.link_regions = []
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72
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73 def plotStart(self, idx):
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74 """Return pair with start coordinates of plot."""
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75 row = idx / self.columns
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76 col = idx % self.columns
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77 x = self.BORDER + col * (self.width + self.SPACE)
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78 y = self.BORDER + row * (self.height + self.SPACE)
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79 return x, y
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80
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81 def plotRecord(self, record):
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82 """Register plotting of a record."""
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83 start_x, start_y = self.plotStart(self.idx)
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84 self.idx += 1
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85 # Register link region.
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86 self.link_regions.append(LinkRegion(
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87 start_x, start_y, start_x + self.width, start_y + self.height,
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88 record.ref, record.start_pos, record.end_pos))
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89
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90
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91 class GridLinks(object):
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92 """Link information for one grid."""
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93
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94 def __init__(self, file_name, link_regions):
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95 self.file_name = file_name
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96 self.link_regions = link_regions
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97
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98
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99 class PlotThumbnailsApp(ngs_roi.app.App):
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100 def __init__(self, args):
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101 # Call parent's constructor.
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102 ngs_roi.app.App.__init__(self, args)
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103 self.prepareOutDir()
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104 # Initialize members.
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105 self.grid = None
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106 self.plot_idx = 0
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107 self.grid_links = []
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108
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109 def run(self):
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110 # Load ROI records.
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111 print >>sys.stderr, 'Loading ROI'
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112
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113 # Create plots.
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114 runner = ngs_roi.app.PlotThumbnailsRunner(self.args)
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115 runner.run()
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116
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117 # Create HTML.
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118 print >>sys.stderr, 'Creating HTML...'
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119 num_plots = self.args.num_cols * self.args.num_rows # plots on grid
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120 for i, roi in enumerate(ngs_roi.io.RoiFile(self.args.in_file)):
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121 if self.args.max_rois > 0 and i >= self.args.max_rois:
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122 break
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123 # Write out old grid (if any) and create new one.
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124 if i % num_plots == 0:
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125 if self.grid:
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126 print >>sys.stderr, ' Writing plot %d...' % self.plot_idx
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127 self.writeGrid()
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128 self.grid = RoiPlotGrid(self.args.plot_width, self.args.plot_height,
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129 self.args.num_cols, self.args.num_rows)
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130 # Put the next plot on the grid.
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131 self.grid.plotRecord(roi)
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132 print >>sys.stderr, ' Writing plot %d...' % self.plot_idx
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133 self.writeGrid() # Write last grid.
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134 self.createHtml(self.args.out_file)
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135 return 0
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136
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137 def writeGrid(self):
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138 """Register writing of grid."""
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139 if not self.grid:
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140 return
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141 # Append grid info.
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142 file_name = 'thumbnail_%d.png' % self.plot_idx
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143 file_name = os.path.join(self.args.out_dir, file_name)
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144 self.plot_idx += 1
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145 self.grid_links.append(GridLinks(os.path.basename(file_name), self.grid.link_regions))
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146
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147 def createHtml(self, file_name):
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148 print >>sys.stderr, 'Writing HTML to %s' % file_name
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149 with open(file_name, 'wb') as f:
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150 f.write('<html><body>\n')
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1
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151 f.write('<h1>ROI Thumbnail Plots</h1>')
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0
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152 for gl in self.grid_links:
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153 vals = (gl.file_name, gl.file_name, self.grid.canvas_width, self.grid.canvas_height)
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154 f.write('<img src="%s" usemap="#%s" width="%d" height="%d" />\n' % vals)
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155 f.write('<map name="%s">\n' % gl.file_name)
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156 for lr in gl.link_regions:
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157 locus = (lr.ref, lr.begin_pos + 1, lr.end_pos)
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158 vals = {'x1': lr.x1, 'x2': lr.x2, 'y1': lr.y1, 'y2': lr.y2,
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159 'title': '%s %d-%d' % locus,
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160 'href': self.buildHref(lr.ref, lr.begin_pos, lr.end_pos),
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161 'onclick': ''}
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162 # Add onclick handler to prevent opening of new window.
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163 vals['target_attr'] = ''
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164 if self.args.link_target:
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165 vals['target_attr'] = ' target="%s"' % self.args.link_target
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166 if self.args.link_type == 'local_igv':
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167 vals['target_attr'] = ' target="empty"'
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168 f.write(' <area shape="rect" coords="%(x1)d,%(y1)d,%(x2)d,%(y2)d" '
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169 'alt="%(title)s" title="%(title)s" href="%(href)s"%(target_attr)s />\n' % vals)
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170 f.write('</map>\n')
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1
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171 f.write('<iframe name="empty" height="0" width="0" src="about:blank"></iframe>\n')
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172 f.write('<div><code>' + str(self.args) + '</code></div></body></html>\n')
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0
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173
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174
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175 def main():
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176 """Program entry point."""
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177 parser = argparse.ArgumentParser(description='Plot ROI file.')
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178 ngs_roi.argparse.addFileArguments(parser)
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179 ngs_roi.argparse.addPlotGridArguments(parser)
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180 ngs_roi.argparse.addLinkArguments(parser)
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181 args = parser.parse_args()
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182 ngs_roi.argparse.applyFileDefaults(args)
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183
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184 app = PlotThumbnailsApp(args)
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185 return app.run()
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186
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187
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188 if __name__ == '__main__':
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189 sys.exit(main())
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