Mercurial > repos > eduardo > annotateviz

annotate jbrowse.py @ 4:92921dfea0b5 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 230f5fe14cc469e56626201a5c377686976d81fc
author eduardo
date Sat, 24 Jun 2017 14:55:25 -0400
parents 7537482eed36
children
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7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty
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1 #!/usr/bin/env python
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2 import argparse
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3 import copy
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4 import hashlib
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5 import json
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6 import logging
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7 import os
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8 import shutil
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9 import struct
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10 import subprocess
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11 import tempfile
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12 import xml.etree.ElementTree as ET
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13 from collections import defaultdict
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14
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15 from Bio.Data import CodonTable
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17 logging.basicConfig(level=logging.INFO)
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18 log = logging.getLogger('jbrowse')
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21 class ColorScaling(object):
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22
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23 COLOR_FUNCTION_TEMPLATE = """
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24 function(feature, variableName, glyphObject, track) {{
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25 var score = {score};
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26 {opacity}
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27 return 'rgba({red}, {green}, {blue}, ' + opacity + ')';
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28 }}
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29 """
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30
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31 COLOR_FUNCTION_TEMPLATE_QUAL = """
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32 function(feature, variableName, glyphObject, track) {{
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33 var search_up = function self(sf, attr){{
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34 if(sf.get(attr) !== undefined){{
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35 return sf.get(attr);
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36 }}
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37 if(sf.parent() === undefined) {{
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38 return;
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39 }}else{{
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40 return self(sf.parent(), attr);
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41 }}
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42 }};
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43
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44 var search_down = function self(sf, attr){{
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45 if(sf.get(attr) !== undefined){{
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46 return sf.get(attr);
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47 }}
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48 if(sf.children() === undefined) {{
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49 return;
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50 }}else{{
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51 var kids = sf.children();
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52 for(var child_idx in kids){{
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53 var x = self(kids[child_idx], attr);
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54 if(x !== undefined){{
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55 return x;
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56 }}
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57 }}
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58 return;
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59 }}
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60 }};
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61
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62 var color = ({user_spec_color} || search_up(feature, 'color') || search_down(feature, 'color') || {auto_gen_color});
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63 var score = (search_up(feature, 'score') || search_down(feature, 'score'));
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64 {opacity}
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65 var result = /^#?([a-f\d]{{2}})([a-f\d]{{2}})([a-f\d]{{2}})$/i.exec(color);
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66 var red = parseInt(result[1], 16);
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67 var green = parseInt(result[2], 16);
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68 var blue = parseInt(result[3], 16);
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69 if(isNaN(opacity) || opacity < 0){{ opacity = 0; }}
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70 return 'rgba(' + red + ',' + green + ',' + blue + ',' + opacity + ')';
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71 }}
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72 """
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73
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74 OPACITY_MATH = {
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75 'linear': """
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76 var opacity = (score - ({min})) / (({max}) - ({min}));
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77 """,
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78 'logarithmic': """
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79 var opacity = (score - ({min})) / (({max}) - ({min}));
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80 opacity = Math.log10(opacity) + Math.log10({max});
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81 """,
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82 'blast': """
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83 var opacity = 0;
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84 if(score == 0.0) {
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85 opacity = 1;
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86 } else{
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87 opacity = (20 - Math.log10(score)) / 180;
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88 }
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89 """
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90 }
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91
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92 BREWER_COLOUR_IDX = 0
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93 BREWER_COLOUR_SCHEMES = [
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94 (166, 206, 227),
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95 (31, 120, 180),
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty
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96 (178, 223, 138),
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97 (51, 160, 44),
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98 (251, 154, 153),
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99 (227, 26, 28),
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100 (253, 191, 111),
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101 (255, 127, 0),
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102 (202, 178, 214),
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103 (106, 61, 154),
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104 (255, 255, 153),
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105 (177, 89, 40),
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106 (228, 26, 28),
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107 (55, 126, 184),
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108 (77, 175, 74),
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109 (152, 78, 163),
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110 (255, 127, 0),
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111 ]
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112
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113 BREWER_DIVERGING_PALLETES = {
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114 'BrBg': ("#543005", "#003c30"),
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115 'PiYg': ("#8e0152", "#276419"),
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116 'PRGn': ("#40004b", "#00441b"),
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117 'PuOr': ("#7f3b08", "#2d004b"),
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118 'RdBu': ("#67001f", "#053061"),
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119 'RdGy': ("#67001f", "#1a1a1a"),
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120 'RdYlBu': ("#a50026", "#313695"),
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121 'RdYlGn': ("#a50026", "#006837"),
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122 'Spectral': ("#9e0142", "#5e4fa2"),
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123 }
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124
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125 def __init__(self):
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126 self.brewer_colour_idx = 0
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127
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128 def rgb_from_hex(self, hexstr):
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129 # http://stackoverflow.com/questions/4296249/how-do-i-convert-a-hex-triplet-to-an-rgb-tuple-and-back
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130 return struct.unpack('BBB', hexstr.decode('hex'))
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131
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132 def min_max_gff(self, gff_file):
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133 min_val = None
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134 max_val = None
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135 with open(gff_file, 'r') as handle:
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136 for line in handle:
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137 try:
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138 value = float(line.split('\t')[5])
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139 min_val = min(value, (min_val or value))
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140 max_val = max(value, (max_val or value))
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141
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142 if value < min_val:
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143 min_val = value
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144
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145 if value > max_val:
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146 max_val = value
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147 except Exception:
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148 pass
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149 return min_val, max_val
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150
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151 def hex_from_rgb(self, r, g, b):
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152 return '#%02x%02x%02x' % (r, g, b)
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153
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154 def _get_colours(self):
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155 r, g, b = self.BREWER_COLOUR_SCHEMES[self.brewer_colour_idx % len(self.BREWER_COLOUR_SCHEMES)]
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156 self.brewer_colour_idx += 1
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157 return r, g, b
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158
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159 def parse_menus(self, track):
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160 trackConfig = {'menuTemplate': [{}, {}, {}]}
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161
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162 if 'menu' in track['menus']:
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163 menu_list = [track['menus']['menu']]
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164 if isinstance(track['menus']['menu'], list):
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165 menu_list = track['menus']['menu']
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166
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167 for m in menu_list:
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168 tpl = {
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169 'action': m['action'],
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170 'label': m.get('label', '{name}'),
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171 'iconClass': m.get('iconClass', 'dijitIconBookmark'),
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172 }
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173 if 'url' in m:
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174 tpl['url'] = m['url']
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175 if 'content' in m:
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176 tpl['content'] = m['content']
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177 if 'title' in m:
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178 tpl['title'] = m['title']
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179
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180 trackConfig['menuTemplate'].append(tpl)
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181
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182 return trackConfig
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183
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184 def parse_colours(self, track, trackFormat, gff3=None):
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185 # Wiggle tracks have a bicolor pallete
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186 trackConfig = {'style': {}}
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187 if trackFormat == 'wiggle':
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188
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189 trackConfig['style']['pos_color'] = track['wiggle']['color_pos']
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190 trackConfig['style']['neg_color'] = track['wiggle']['color_neg']
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191
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192 if trackConfig['style']['pos_color'] == '__auto__':
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193 trackConfig['style']['neg_color'] = self.hex_from_rgb(*self._get_colours())
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194 trackConfig['style']['pos_color'] = self.hex_from_rgb(*self._get_colours())
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195
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196 # Wiggle tracks can change colour at a specified place
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197 bc_pivot = track['wiggle']['bicolor_pivot']
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198 if bc_pivot not in ('mean', 'zero'):
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199 # The values are either one of those two strings
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200 # or a number
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201 bc_pivot = float(bc_pivot)
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202 trackConfig['bicolor_pivot'] = bc_pivot
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203 elif 'scaling' in track:
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204 if track['scaling']['method'] == 'ignore':
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205 if track['scaling']['scheme']['color'] != '__auto__':
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206 trackConfig['style']['color'] = track['scaling']['scheme']['color']
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207 else:
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208 trackConfig['style']['color'] = self.hex_from_rgb(*self._get_colours())
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209 else:
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210 # Scored method
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211 algo = track['scaling']['algo']
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212 # linear, logarithmic, blast
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213 scales = track['scaling']['scales']
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214 # type __auto__, manual (min, max)
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215 scheme = track['scaling']['scheme']
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216 # scheme -> (type (opacity), color)
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217 # ==================================
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218 # GENE CALLS OR BLAST
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219 # ==================================
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220 if trackFormat == 'blast':
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221 red, green, blue = self._get_colours()
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222 color_function = self.COLOR_FUNCTION_TEMPLATE.format(**{
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223 'score': "feature._parent.get('score')",
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224 'opacity': self.OPACITY_MATH['blast'],
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225 'red': red,
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226 'green': green,
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227 'blue': blue,
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228 })
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229 trackConfig['style']['color'] = color_function.replace('\n', '')
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230 elif trackFormat == 'gene_calls':
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231 # Default values, based on GFF3 spec
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232 min_val = 0
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233 max_val = 1000
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234 # Get min/max and build a scoring function since JBrowse doesn't
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235 if scales['type'] == 'automatic' or scales['type'] == '__auto__':
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236 min_val, max_val = self.min_max_gff(gff3)
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237 else:
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238 min_val = scales.get('min', 0)
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239 max_val = scales.get('max', 1000)
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240
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241 if scheme['color'] == '__auto__':
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242 user_color = 'undefined'
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243 auto_color = "'%s'" % self.hex_from_rgb(*self._get_colours())
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244 elif scheme['color'].startswith('#'):
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245 user_color = "'%s'" % self.hex_from_rgb(*self.rgb_from_hex(scheme['color'][1:]))
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246 auto_color = 'undefined'
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247 else:
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248 user_color = 'undefined'
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249 auto_color = "'%s'" % self.hex_from_rgb(*self._get_colours())
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250
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251 color_function = self.COLOR_FUNCTION_TEMPLATE_QUAL.format(**{
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252 'opacity': self.OPACITY_MATH[algo].format(**{'max': max_val, 'min': min_val}),
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253 'user_spec_color': user_color,
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254 'auto_gen_color': auto_color,
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255 })
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256
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257 trackConfig['style']['color'] = color_function.replace('\n', '')
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258 return trackConfig
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259
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260
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261 def etree_to_dict(t):
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262 d = {t.tag: {} if t.attrib else None}
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263 children = list(t)
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264 if children:
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265 dd = defaultdict(list)
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266 for dc in map(etree_to_dict, children):
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267 for k, v in dc.iteritems():
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268 dd[k].append(v)
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269 d = {t.tag: {k: v[0] if len(v) == 1 else v for k, v in dd.iteritems()}}
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270 if t.attrib:
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271 d[t.tag].update(('@' + k, v) for k, v in t.attrib.iteritems())
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272 if t.text:
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273 text = t.text.strip()
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274 if children or t.attrib:
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275 if text:
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276 d[t.tag]['#text'] = text
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277 else:
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278 d[t.tag] = text
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279 return d
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280
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281
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282 # score comes from feature._parent.get('score') or feature.get('score')
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283
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284 INSTALLED_TO = os.path.dirname(os.path.realpath(__file__))
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285
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286
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287 class JbrowseConnector(object):
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288
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289 def __init__(self, jbrowse, outdir, genomes, standalone=False, gencode=1):
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290 self.TN_TABLE = {
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291 'gff3': '--gff',
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292 'gff': '--gff',
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293 'bed': '--bed',
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294 'genbank': '--gbk',
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295 }
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296
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297 self.cs = ColorScaling()
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298 self.jbrowse = jbrowse
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299 self.outdir = outdir
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300 self.genome_paths = genomes
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301 self.standalone = standalone
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302 self.gencode = gencode
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303 self.tracksToIndex = []
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304
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305 if standalone:
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306 self.clone_jbrowse(self.jbrowse, self.outdir)
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307 else:
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308 try:
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309 os.makedirs(self.outdir)
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310 except OSError:
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311 # Ignore if the folder exists
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312 pass
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313
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314 self.process_genomes()
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315 self.update_gencode()
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316
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317 def update_gencode(self):
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318 table = CodonTable.unambiguous_dna_by_id[int(self.gencode)]
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319 trackList = os.path.join(self.outdir, 'data', 'trackList.json')
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320 with open(trackList, 'r') as handle:
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321 trackListData = json.load(handle)
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322
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323 trackListData['tracks'][0].update({
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324 'codonStarts': table.start_codons,
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325 'codonStops': table.stop_codons,
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326 'codonTable': table.forward_table,
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327 })
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328
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329 with open(trackList, 'w') as handle:
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330 json.dump(trackListData, handle, indent=2)
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331
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332 def subprocess_check_call(self, command):
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333 log.debug('cd %s && %s', self.outdir, ' '.join(command))
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334 subprocess.check_call(command, cwd=self.outdir)
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335
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336 def _jbrowse_bin(self, command):
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337 return os.path.realpath(os.path.join(self.jbrowse, 'bin', command))
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338
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339 def process_genomes(self):
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340 for genome_path in self.genome_paths:
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341 self.subprocess_check_call([
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342 'perl', self._jbrowse_bin('prepare-refseqs.pl'),
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343 '--fasta', genome_path])
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344
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345 def generate_names(self):
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346 # Generate names
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347
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348 args = [
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349 'perl', self._jbrowse_bin('generate-names.pl'),
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350 '--hashBits', '16'
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351 ]
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352
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353 tracks = ','.join(self.tracksToIndex)
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354
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355 if tracks:
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356 args += ['--tracks', tracks]
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357 else:
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358 # No tracks to index, index only the refseq
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359 args += ['--tracks', 'DNA']
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360
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361 self.subprocess_check_call(args)
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362
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363 def _add_json(self, json_data):
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364
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365 cmd = [
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366 'perl', self._jbrowse_bin('add-json.pl'),
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367 json.dumps(json_data),
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368 os.path.join('data', 'trackList.json')
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369 ]
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370 self.subprocess_check_call(cmd)
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371
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372 def _add_track_json(self, json_data):
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373 if len(json_data.keys()) == 0:
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374 return
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375
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376 tmp = tempfile.NamedTemporaryFile(delete=False)
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377 tmp.write(json.dumps(json_data))
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378 tmp.close()
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379 cmd = ['perl', self._jbrowse_bin('add-track-json.pl'), tmp.name,
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380 os.path.join('data', 'trackList.json')]
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381 self.subprocess_check_call(cmd)
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382 os.unlink(tmp.name)
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383
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384 def _blastxml_to_gff3(self, xml, min_gap=10):
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385 gff3_unrebased = tempfile.NamedTemporaryFile(delete=False)
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386 cmd = ['python', os.path.join(INSTALLED_TO, 'blastxml_to_gapped_gff3.py'),
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387 '--trim', '--trim_end', '--min_gap', str(min_gap), xml]
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388 log.debug('cd %s && %s > %s', self.outdir, ' '.join(cmd), gff3_unrebased.name)
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389 subprocess.check_call(cmd, cwd=self.outdir, stdout=gff3_unrebased)
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390 gff3_unrebased.close()
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391 return gff3_unrebased.name
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392
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393 def add_blastxml(self, data, trackData, blastOpts, **kwargs):
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394 gff3 = self._blastxml_to_gff3(data, min_gap=blastOpts['min_gap'])
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395
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396 if 'parent' in blastOpts and blastOpts['parent'] != 'None':
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397 gff3_rebased = tempfile.NamedTemporaryFile(delete=False)
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398 cmd = ['python', os.path.join(INSTALLED_TO, 'gff3_rebase.py')]
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399 if blastOpts.get('protein', 'false') == 'true':
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400 cmd.append('--protein2dna')
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401 cmd.extend([os.path.realpath(blastOpts['parent']), gff3])
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402 log.debug('cd %s && %s > %s', self.outdir, ' '.join(cmd), gff3_rebased.name)
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403 subprocess.check_call(cmd, cwd=self.outdir, stdout=gff3_rebased)
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404 gff3_rebased.close()
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405
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406 # Replace original gff3 file
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407 shutil.copy(gff3_rebased.name, gff3)
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408 os.unlink(gff3_rebased.name)
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409
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410 config = {
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411 'glyph': 'JBrowse/View/FeatureGlyph/Segments',
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412 "category": trackData['category'],
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413 }
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414
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415 clientConfig = trackData['style']
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416
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417 cmd = ['perl', self._jbrowse_bin('flatfile-to-json.pl'),
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418 '--gff', gff3,
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419 '--trackLabel', trackData['label'],
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420 '--key', trackData['key'],
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421 '--clientConfig', json.dumps(clientConfig),
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422 '--config', json.dumps(config),
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423 '--trackType', 'JBrowse/View/Track/CanvasFeatures'
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424 ]
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425
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426 self.subprocess_check_call(cmd)
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427 os.unlink(gff3)
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428
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429 if blastOpts.get('index', 'false') == 'true':
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430 self.tracksToIndex.append("%s" % trackData['label'])
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431
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432 def add_bigwig(self, data, trackData, wiggleOpts, **kwargs):
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433 dest = os.path.join('data', 'raw', trackData['label'] + '.bw')
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434 cmd = ['ln', data, dest]
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435 self.subprocess_check_call(cmd)
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436
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437 trackData.update({
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438 "urlTemplate": os.path.join('..', dest),
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439 "storeClass": "JBrowse/Store/SeqFeature/BigWig",
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440 "type": "JBrowse/View/Track/Wiggle/Density",
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441 })
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442
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443 trackData['type'] = wiggleOpts['type']
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444 trackData['variance_band'] = True if wiggleOpts['variance_band'] == 'true' else False
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445
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446 if 'min' in wiggleOpts and 'max' in wiggleOpts:
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447 trackData['min_score'] = wiggleOpts['min']
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448 trackData['max_score'] = wiggleOpts['max']
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449 else:
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450 trackData['autoscale'] = wiggleOpts.get('autoscale', 'local')
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451
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452 self._add_track_json(trackData)
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453
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454 def add_bam(self, data, trackData, bamOpts, bam_index=None, **kwargs):
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455 dest = os.path.join('data', 'raw', trackData['label'] + '.bam')
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456 cmd = ['ln', '-s', os.path.realpath(data), dest]
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eduardo
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diff changeset
457 self.subprocess_check_call(cmd)
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458
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diff changeset
459 cmd = ['ln', '-s', os.path.realpath(bam_index), dest + '.bai']
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diff changeset
460 self.subprocess_check_call(cmd)
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461
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diff changeset
462 trackData.update({
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diff changeset
463 "urlTemplate": os.path.join('..', dest),
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464 "type": "JBrowse/View/Track/Alignments2",
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465 "storeClass": "JBrowse/Store/SeqFeature/BAM",
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466 })
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diff changeset
467
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468 self._add_track_json(trackData)
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469
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470 if bamOpts.get('auto_snp', 'false') == 'true':
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471 trackData2 = copy.copy(trackData)
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diff changeset
472 trackData2.update({
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473 "type": "JBrowse/View/Track/SNPCoverage",
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474 "key": trackData['key'] + " - SNPs/Coverage",
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475 "label": trackData['label'] + "_autosnp",
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476 })
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477 self._add_track_json(trackData2)
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478
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479 def add_vcf(self, data, trackData, vcfOpts={}, **kwargs):
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480 dest = os.path.join('data', 'raw', trackData['label'] + '.vcf')
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481 # ln?
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482 cmd = ['ln', '-s', data, dest]
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483 self.subprocess_check_call(cmd)
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484 cmd = ['bgzip', dest]
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485 self.subprocess_check_call(cmd)
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486 cmd = ['tabix', '-p', 'vcf', dest + '.gz']
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487 self.subprocess_check_call(cmd)
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488
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489 trackData.update({
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490 "urlTemplate": os.path.join('..', dest + '.gz'),
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491 "type": "JBrowse/View/Track/HTMLVariants",
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492 "storeClass": "JBrowse/Store/SeqFeature/VCFTabix",
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493 })
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494 self._add_track_json(trackData)
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495
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496 def add_features(self, data, format, trackData, gffOpts, **kwargs):
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497 cmd = [
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498 'perl', self._jbrowse_bin('flatfile-to-json.pl'),
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499 self.TN_TABLE.get(format, 'gff'),
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diff changeset
500 data,
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501 '--trackLabel', trackData['label'],
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502 # '--trackType', 'JBrowse/View/Track/CanvasFeatures',
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503 '--key', trackData['key']
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504 ]
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505
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506 config = copy.copy(trackData)
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507 clientConfig = trackData['style']
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diff changeset
508 del config['style']
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509
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510 if 'match' in gffOpts:
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511 config['glyph'] = 'JBrowse/View/FeatureGlyph/Segments'
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512 cmd += ['--type', gffOpts['match']]
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513
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514 cmd += ['--clientConfig', json.dumps(clientConfig),
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515 ]
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516
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517 if 'trackType' in gffOpts:
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518 cmd += [
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519 '--trackType', gffOpts['trackType']
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520 ]
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diff changeset
521 else:
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522 cmd += [
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523 '--trackType', 'JBrowse/View/Track/CanvasFeatures'
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524 ]
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diff changeset
525
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526 cmd.extend(['--config', json.dumps(config)])
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527
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diff changeset
528 self.subprocess_check_call(cmd)
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diff changeset
529
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530 if gffOpts.get('index', 'false') == 'true':
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parents:
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531 self.tracksToIndex.append("%s" % trackData['label'])
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diff changeset
532
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parents:
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533 def process_annotations(self, track):
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parents:
diff changeset
534 outputTrackConfig = {
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parents:
diff changeset
535 'style': {
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536 'label': track['style'].get('label', 'description'),
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537 'className': track['style'].get('className', 'feature'),
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parents:
diff changeset
538 'description': track['style'].get('description', ''),
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diff changeset
539 },
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540 'category': track['category'],
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diff changeset
541 }
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542
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543 for i, (dataset_path, dataset_ext, track_human_label) in enumerate(track['trackfiles']):
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parents:
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544 log.info('Processing %s / %s', track['category'], track_human_label)
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545 outputTrackConfig['key'] = track_human_label
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parents:
diff changeset
546 hashData = [dataset_path, track_human_label, track['category']]
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547 outputTrackConfig['label'] = hashlib.md5('|'.join(hashData)).hexdigest() + '_%s' % i
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548
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549 # Colour parsing is complex due to different track types having
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550 # different colour options.
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551 colourOptions = self.cs.parse_colours(track['conf']['options'], track['format'], gff3=dataset_path)
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552 # This used to be done with a dict.update() call, however that wiped out any previous style settings...
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553 for key in colourOptions:
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554 if key == 'style':
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555 for subkey in colourOptions['style']:
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556 outputTrackConfig['style'][subkey] = colourOptions['style'][subkey]
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557 else:
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558 outputTrackConfig[key] = colourOptions[key]
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559
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560 menus = self.cs.parse_menus(track['conf']['options'])
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561 outputTrackConfig.update(menus)
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562
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563 # import pprint; pprint.pprint(track)
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564 # import sys; sys.exit()
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565 if dataset_ext in ('gff', 'gff3', 'bed'):
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566 self.add_features(dataset_path, dataset_ext, outputTrackConfig,
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567 track['conf']['options']['gff'])
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568 elif dataset_ext == 'bigwig':
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569 self.add_bigwig(dataset_path, outputTrackConfig,
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570 track['conf']['options']['wiggle'])
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571 elif dataset_ext == 'bam':
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572 real_indexes = track['conf']['options']['pileup']['bam_indices']['bam_index']
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573 if not isinstance(real_indexes, list):
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574 # <bam_indices>
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575 # <bam_index>/path/to/a.bam.bai</bam_index>
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576 # </bam_indices>
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577 #
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578 # The above will result in the 'bam_index' key containing a
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579 # string. If there are two or more indices, the container
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580 # becomes a list. Fun!
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581 real_indexes = [real_indexes]
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582
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583 self.add_bam(dataset_path, outputTrackConfig,
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584 track['conf']['options']['pileup'],
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585 bam_index=real_indexes[i])
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586 elif dataset_ext == 'blastxml':
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587 self.add_blastxml(dataset_path, outputTrackConfig, track['conf']['options']['blast'])
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588 elif dataset_ext == 'vcf':
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589 self.add_vcf(dataset_path, outputTrackConfig)
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590
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591 # Return non-human label for use in other fields
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592 yield outputTrackConfig['label']
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593
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594 def add_final_data(self, data):
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595 viz_data = {}
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596 if len(data['visibility']['default_on']) > 0:
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597 viz_data['defaultTracks'] = ','.join(data['visibility']['default_on'])
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598
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599 if len(data['visibility']['always']) > 0:
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600 viz_data['alwaysOnTracks'] = ','.join(data['visibility']['always'])
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601
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602 if len(data['visibility']['force']) > 0:
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603 viz_data['forceTracks'] = ','.join(data['visibility']['force'])
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604
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605 generalData = {}
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606 if data['general']['aboutDescription'] is not None:
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607 generalData['aboutThisBrowser'] = {'description': data['general']['aboutDescription'].strip()}
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608
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609 generalData['view'] = {
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610 'trackPadding': data['general']['trackPadding']
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611 }
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612 generalData['shareLink'] = (data['general']['shareLink'] == 'true')
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613 generalData['show_tracklist'] = (data['general']['show_tracklist'] == 'true')
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614 generalData['show_nav'] = (data['general']['show_nav'] == 'true')
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615 generalData['show_overview'] = (data['general']['show_overview'] == 'true')
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616 generalData['show_menu'] = (data['general']['show_menu'] == 'true')
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617 generalData['hideGenomeOptions'] = (data['general']['hideGenomeOptions'] == 'true')
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618
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619 viz_data.update(generalData)
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620 self._add_json(viz_data)
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621
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622 def clone_jbrowse(self, jbrowse_dir, destination):
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623 """Clone a JBrowse directory into a destination directory.
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624 """
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625 # JBrowse seems to have included some bad symlinks, cp ignores bad symlinks
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626 # unlike copytree
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627 cmd = ['cp', '-r', os.path.join(jbrowse_dir, '.'), destination]
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628 log.debug(' '.join(cmd))
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629 subprocess.check_call(cmd)
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630 cmd = ['mkdir', '-p', os.path.join(destination, 'data', 'raw')]
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631 log.debug(' '.join(cmd))
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632 subprocess.check_call(cmd)
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633
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634 # http://unix.stackexchange.com/a/38691/22785
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635 # JBrowse releases come with some broken symlinks
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636 cmd = ['find', destination, '-type', 'l', '-xtype', 'l', '-exec', 'rm', "'{}'", '+']
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637 log.debug(' '.join(cmd))
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638 subprocess.check_call(cmd)
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639
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640
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641 if __name__ == '__main__':
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642 parser = argparse.ArgumentParser(description="", epilog="")
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643 parser.add_argument('xml', type=file, help='Track Configuration')
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644
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645 parser.add_argument('--jbrowse', help='Folder containing a jbrowse release')
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646 parser.add_argument('--outdir', help='Output directory', default='out')
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647 parser.add_argument('--standalone', help='Standalone mode includes a copy of JBrowse', action='store_true')
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648 args = parser.parse_args()
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649
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650 tree = ET.parse(args.xml.name)
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651 root = tree.getroot()
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652
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653 jc = JbrowseConnector(
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654 jbrowse=args.jbrowse,
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655 outdir=args.outdir,
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656 genomes=[os.path.realpath(x.text) for x in root.findall('metadata/genomes/genome')],
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657 standalone=args.standalone,
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658 gencode=root.find('metadata/gencode').text
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659 )
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660
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661 extra_data = {
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662 'visibility': {
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663 'default_on': [],
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664 'default_off': [],
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665 'force': [],
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666 'always': [],
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667 },
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668 'general': {
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669 'defaultLocation': root.find('metadata/general/defaultLocation').text,
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670 'trackPadding': int(root.find('metadata/general/trackPadding').text),
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671 'shareLink': root.find('metadata/general/shareLink').text,
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672 'aboutDescription': root.find('metadata/general/aboutDescription').text,
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673 'show_tracklist': root.find('metadata/general/show_tracklist').text,
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674 'show_nav': root.find('metadata/general/show_nav').text,
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675 'show_overview': root.find('metadata/general/show_overview').text,
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676 'show_menu': root.find('metadata/general/show_menu').text,
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677 'hideGenomeOptions': root.find('metadata/general/hideGenomeOptions').text,
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678 }
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679 }
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680 for track in root.findall('tracks/track'):
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681 track_conf = {}
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682 track_conf['trackfiles'] = [
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683 (os.path.realpath(x.attrib['path']), x.attrib['ext'], x.attrib['label'])
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684 for x in track.findall('files/trackFile')
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685 ]
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686
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687 track_conf['category'] = track.attrib['cat']
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688 track_conf['format'] = track.attrib['format']
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689 try:
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690 # Only pertains to gff3 + blastxml. TODO?
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691 track_conf['style'] = {t.tag: t.text for t in track.find('options/style')}
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692 except TypeError:
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693 track_conf['style'] = {}
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694 pass
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695 track_conf['conf'] = etree_to_dict(track.find('options'))
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696 keys = jc.process_annotations(track_conf)
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697
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698 for key in keys:
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699 extra_data['visibility'][track.attrib.get('visibility', 'default_off')].append(key)
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700
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701 jc.add_final_data(extra_data)
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702 jc.generate_names()