annotate jbrowse.py @ 5:ae9382cfb6ac draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
author iuc
date Sat, 25 Jun 2016 15:06:43 -0400
parents 7342f467507b
children ad4b9d7eae6a
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1 #!/usr/bin/env python
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2 import os
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3 import copy
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4 import argparse
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5 import subprocess
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6 import hashlib
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7 import struct
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8 import tempfile
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9 import shutil
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10 import json
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11 from Bio.Data import CodonTable
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12 import xml.etree.ElementTree as ET
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13 import logging
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14 from collections import defaultdict
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15 logging.basicConfig(level=logging.INFO)
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16 log = logging.getLogger('jbrowse')
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18
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19 class ColorScaling(object):
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20
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21 COLOR_FUNCTION_TEMPLATE = """
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22 function(feature, variableName, glyphObject, track) {{
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23 var score = {score};
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24 {opacity}
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25 return 'rgba({red}, {green}, {blue}, ' + opacity + ')';
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26 }}
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27 """
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28
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29 COLOR_FUNCTION_TEMPLATE_QUAL = """
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30 function(feature, variableName, glyphObject, track) {{
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31 var search_up = function self(sf, attr){{
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32 if(sf.get(attr) !== undefined){{
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33 return sf.get(attr);
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34 }}
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35 if(sf.parent() === undefined) {{
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36 return;
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37 }}else{{
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38 return self(sf.parent(), attr);
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39 }}
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40 }};
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41
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42 var search_down = function self(sf, attr){{
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43 if(sf.get(attr) !== undefined){{
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44 return sf.get(attr);
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45 }}
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46 if(sf.children() === undefined) {{
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47 return;
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48 }}else{{
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49 var kids = sf.children();
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50 for(var child_idx in kids){{
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51 var x = self(kids[child_idx], attr);
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52 if(x !== undefined){{
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53 return x;
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54 }}
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55 }}
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56 return;
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57 }}
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58 }};
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59
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60 var color = ({user_spec_color} || search_up(feature, 'color') || search_down(feature, 'color') || {auto_gen_color});
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61 var score = (search_up(feature, 'score') || search_down(feature, 'score'));
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62 {opacity}
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63 var result = /^#?([a-f\d]{{2}})([a-f\d]{{2}})([a-f\d]{{2}})$/i.exec(color);
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64 var red = parseInt(result[1], 16);
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65 var green = parseInt(result[2], 16);
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66 var blue = parseInt(result[3], 16);
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67 if(isNaN(opacity) || opacity < 0){{ opacity = 0; }}
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68 return 'rgba(' + red + ',' + green + ',' + blue + ',' + opacity + ')';
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69 }}
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70 """
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71
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72 OPACITY_MATH = {
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73 'linear': """
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74 var opacity = (score - ({min})) / (({max}) - ({min}));
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75 """,
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76 'logarithmic': """
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77 var opacity = (score - ({min})) / (({max}) - ({min}));
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78 opacity = Math.log10(opacity) + Math.log10({max});
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79 """,
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80 'blast': """
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81 var opacity = 0;
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82 if(score == 0.0) {{
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83 opacity = 1;
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84 }} else {{
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85 opacity = (20 - Math.log10(score)) / 180;
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86 }}
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87 """
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88 }
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89
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90 BREWER_COLOUR_IDX = 0
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91 BREWER_COLOUR_SCHEMES = [
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92 (166, 206, 227),
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93 (31, 120, 180),
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94 (178, 223, 138),
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95 (51, 160, 44),
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96 (251, 154, 153),
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97 (227, 26, 28),
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98 (253, 191, 111),
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99 (255, 127, 0),
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100 (202, 178, 214),
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101 (106, 61, 154),
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102 (255, 255, 153),
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103 (177, 89, 40),
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104 (228, 26, 28),
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105 (55, 126, 184),
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106 (77, 175, 74),
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107 (152, 78, 163),
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108 (255, 127, 0),
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109 ]
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110
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111 BREWER_DIVERGING_PALLETES = {
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112 'BrBg': ("#543005", "#003c30"),
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113 'PiYg': ("#8e0152", "#276419"),
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114 'PRGn': ("#40004b", "#00441b"),
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115 'PuOr': ("#7f3b08", "#2d004b"),
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116 'RdBu': ("#67001f", "#053061"),
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117 'RdGy': ("#67001f", "#1a1a1a"),
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118 'RdYlBu': ("#a50026", "#313695"),
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119 'RdYlGn': ("#a50026", "#006837"),
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120 'Spectral': ("#9e0142", "#5e4fa2"),
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121 }
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122
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123 def __init__(self):
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124 self.brewer_colour_idx = 0
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125
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126 def rgb_from_hex(self, hexstr):
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127 # http://stackoverflow.com/questions/4296249/how-do-i-convert-a-hex-triplet-to-an-rgb-tuple-and-back
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128 return struct.unpack('BBB',hexstr.decode('hex'))
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129
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130 def min_max_gff(self, gff_file):
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131 min_val = None
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132 max_val = None
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133 with open(gff_file, 'r') as handle:
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134 for line in handle:
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135 try:
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136 value = float(line.split('\t')[5])
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137 min_val = min(value, (min_val or value))
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138 max_val = max(value, (max_val or value))
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139
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140 if value < min_val:
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141 min_val = value
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142
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143 if value > max_val:
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144 max_val = value
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145 except Exception:
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146 pass
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147 return min_val, max_val
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148
3
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149 def hex_from_rgb(self, r, g, b):
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150 return '#%02x%02x%02x' % (r, g, b)
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151
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152 def _get_colours(self):
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153 r, g, b = self.BREWER_COLOUR_SCHEMES[self.brewer_colour_idx % len(self.BREWER_COLOUR_SCHEMES)]
3
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154 self.brewer_colour_idx += 1
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155 return r, g, b
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156
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157 def parse_colours(self, track, trackFormat, gff3=None):
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158 # Wiggle tracks have a bicolor pallete
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159 trackConfig = {'style': {}}
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160 if trackFormat == 'wiggle':
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161
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162 trackConfig['style']['pos_color'] = track['wiggle']['color_pos']
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163 trackConfig['style']['neg_color'] = track['wiggle']['color_neg']
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164
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165 if trackConfig['style']['pos_color'] == '__auto__':
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166 trackConfig['style']['neg_color'] = self.hex_from_rgb(*self._get_colours())
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167 trackConfig['style']['pos_color'] = self.hex_from_rgb(*self._get_colours())
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168
1
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169
3
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170 # Wiggle tracks can change colour at a specified place
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171 bc_pivot = track['wiggle']['bicolor_pivot']
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172 if bc_pivot not in ('mean', 'zero'):
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173 # The values are either one of those two strings
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174 # or a number
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175 bc_pivot = float(bc_pivot)
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176 trackConfig['bicolor_pivot'] = bc_pivot
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177 elif 'scaling' in track:
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178 if track['scaling']['method'] == 'ignore':
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179 if track['scaling']['scheme']['color'] != '__auto__':
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180 trackConfig['style']['color'] = track['scaling']['scheme']['color']
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181 else:
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182 trackConfig['style']['color'] = self.hex_from_rgb(*self._get_colours())
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183 else:
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184 # Scored method
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185 algo = track['scaling']['algo']
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186 # linear, logarithmic, blast
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187 scales = track['scaling']['scales']
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188 # type __auto__, manual (min, max)
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189 scheme = track['scaling']['scheme']
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190 # scheme -> (type (opacity), color)
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191 # ==================================
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192 # GENE CALLS OR BLAST
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193 # ==================================
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194 if trackFormat == 'blast':
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195 red, green, blue = self._get_colours()
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196 color_function = self.COLOR_FUNCTION_TEMPLATE.format(**{
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197 'score': "feature._parent.get('score')",
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198 'opacity': self.OPACITY_MATH['blast'],
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199 'red': red,
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200 'green': green,
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201 'blue': blue,
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202 })
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203 trackConfig['style']['color'] = color_function.replace('\n', '')
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204 elif trackFormat == 'gene_calls':
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205 # Default values, based on GFF3 spec
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206 min_val = 0
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207 max_val = 1000
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208 # Get min/max and build a scoring function since JBrowse doesn't
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209 if scales['type'] == 'automatic' or scales['type'] == '__auto__':
3
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210 min_val, max_val = self.min_max_gff(gff3)
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211 else:
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212 min_val = scales.get('min', 0)
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213 max_val = scales.get('max', 1000)
3
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214
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215 if scheme['color'] == '__auto__':
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216 user_color = 'undefined'
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217 auto_color = "'%s'" % self.hex_from_rgb(*self._get_colours())
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218 elif scheme['color'].startswith('#'):
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219 user_color = "'%s'" % self.hex_from_rgb(*self.rgb_from_hex(scheme['color'][1:]))
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220 auto_color = 'undefined'
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221 else:
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222 user_color = 'undefined'
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223 auto_color = "'%s'" % self.hex_from_rgb(*self._get_colours())
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224
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225 color_function = self.COLOR_FUNCTION_TEMPLATE_QUAL.format(**{
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226 'opacity': self.OPACITY_MATH[algo].format(**{'max': max_val,'min': min_val}),
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227 'user_spec_color': user_color,
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228 'auto_gen_color': auto_color,
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229 })
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230
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231 trackConfig['style']['color'] = color_function.replace('\n', '')
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232 return trackConfig
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233
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234
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235 def etree_to_dict(t):
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236 d = {t.tag: {} if t.attrib else None}
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237 children = list(t)
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238 if children:
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239 dd = defaultdict(list)
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240 for dc in map(etree_to_dict, children):
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241 for k, v in dc.iteritems():
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242 dd[k].append(v)
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243 d = {t.tag: {k:v[0] if len(v) == 1 else v for k, v in dd.iteritems()}}
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244 if t.attrib:
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245 d[t.tag].update(('@' + k, v) for k, v in t.attrib.iteritems())
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246 if t.text:
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247 text = t.text.strip()
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248 if children or t.attrib:
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249 if text:
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250 d[t.tag]['#text'] = text
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251 else:
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252 d[t.tag] = text
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253 return d
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254
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255
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256 # score comes from feature._parent.get('score') or feature.get('score')
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257
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258 INSTALLED_TO = os.path.dirname(os.path.realpath(__file__))
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259
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260
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261 class JbrowseConnector(object):
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262
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263 def __init__(self, jbrowse, outdir, genomes, standalone=False, gencode=1):
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264 self.TN_TABLE = {
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265 'gff3': '--gff',
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266 'gff': '--gff',
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267 'bed': '--bed',
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268 'genbank': '--gbk',
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269 }
3
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270
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271 self.cs = ColorScaling()
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272 self.jbrowse = jbrowse
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273 self.outdir = outdir
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274 self.genome_paths = genomes
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275 self.standalone = standalone
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276 self.gencode = gencode
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277
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278 if standalone:
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279 self.clone_jbrowse(self.jbrowse, self.outdir)
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280 else:
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281 try:
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282 os.makedirs(self.outdir)
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283 except OSError:
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284 # Ignore if the folder exists
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285 pass
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286
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287 self.process_genomes()
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288 self.update_gencode()
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289
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290 def update_gencode(self):
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291 table = CodonTable.unambiguous_dna_by_id[int(self.gencode)]
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292 trackList = os.path.join(self.outdir, 'data', 'trackList.json')
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293 with open(trackList, 'r') as handle:
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294 trackListData = json.load(handle)
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295
3
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296 trackListData['tracks'][0].update({
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297 'codonStarts': table.start_codons,
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298 'codonStops': table.stop_codons,
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299 'codonTable': table.forward_table,
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300 })
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301
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302 with open(trackList, 'w') as handle:
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303 json.dump(trackListData, handle, indent=2)
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304
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305
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306 def subprocess_check_call(self, command):
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307 log.debug('cd %s && %s', self.outdir, ' '.join(command))
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308 subprocess.check_call(command, cwd=self.outdir)
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309
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310 def _jbrowse_bin(self, command):
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311 return os.path.realpath(os.path.join(self.jbrowse, 'bin', command))
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312
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313 def process_genomes(self):
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314 for genome_path in self.genome_paths:
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315 self.subprocess_check_call([
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316 'perl', self._jbrowse_bin('prepare-refseqs.pl'),
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317 '--fasta', genome_path])
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318
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319 # Generate name
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320 # self.subprocess_check_call([
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321 # 'perl', self._jbrowse_bin('generate-names.pl'),
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322 # '--hashBits', '16'
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323 # ])
3
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324
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325 def _add_json(self, json_data):
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326
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327 cmd = [
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328 'perl', self._jbrowse_bin('add-json.pl'),
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329 json.dumps(json_data),
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330 os.path.join('data', 'trackList.json')
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331 ]
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332 self.subprocess_check_call(cmd)
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333
3
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334 def _add_track_json(self, json_data):
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335 if len(json_data.keys()) == 0:
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336 return
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337
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338 tmp = tempfile.NamedTemporaryFile(delete=False)
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339 tmp.write(json.dumps(json_data))
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340 tmp.close()
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341 cmd = ['perl', self._jbrowse_bin('add-track-json.pl'), tmp.name,
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342 os.path.join('data', 'trackList.json')]
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343 self.subprocess_check_call(cmd)
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344 os.unlink(tmp.name)
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345
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346
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347 def _blastxml_to_gff3(self, xml, min_gap=10):
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348 gff3_unrebased = tempfile.NamedTemporaryFile(delete=False)
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349 cmd = ['python', os.path.join(INSTALLED_TO, 'blastxml_to_gapped_gff3.py'),
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350 '--trim', '--trim_end', '--min_gap', str(min_gap), xml]
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351 log.debug('cd %s && %s > %s', self.outdir, ' '.join(cmd), gff3_unrebased.name)
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352 subprocess.check_call(cmd, cwd=self.outdir, stdout=gff3_unrebased)
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353 gff3_unrebased.close()
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354 return gff3_unrebased.name
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355
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356 def add_blastxml(self, data, trackData, blastOpts, **kwargs):
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357 gff3 = self._blastxml_to_gff3(data, min_gap=blastOpts['min_gap'])
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358
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359 if 'parent' in blastOpts and blastOpts['parent'] != 'None':
3
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360 gff3_rebased = tempfile.NamedTemporaryFile(delete=False)
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361 cmd = ['python', os.path.join(INSTALLED_TO, 'gff3_rebase.py')]
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362 if blastOpts.get('protein', 'false') == 'true':
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363 cmd.append('--protein2dna')
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364 cmd.extend([os.path.realpath(blastOpts['parent']), gff3])
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365 log.debug('cd %s && %s > %s', self.outdir, ' '.join(cmd), gff3_rebased.name)
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366 subprocess.check_call(cmd, cwd=self.outdir, stdout=gff3_rebased)
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367 gff3_rebased.close()
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368
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369 # Replace original gff3 file
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370 shutil.copy(gff3_rebased.name, gff3)
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371 os.unlink(gff3_rebased.name)
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372
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373 config = {
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374 'glyph': 'JBrowse/View/FeatureGlyph/Segments',
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375 "category": trackData['category'],
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376 }
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377
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378 clientConfig = trackData['style']
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379
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380 cmd = ['perl', self._jbrowse_bin('flatfile-to-json.pl'),
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381 '--gff', gff3,
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382 '--trackLabel', trackData['label'],
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383 '--key', trackData['key'],
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384 '--clientConfig', json.dumps(clientConfig),
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385 '--config', json.dumps(config),
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386 '--trackType', 'JBrowse/View/Track/CanvasFeatures'
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387 ]
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388
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389 self.subprocess_check_call(cmd)
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390 os.unlink(gff3)
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391
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392 def add_bigwig(self, data, trackData, wiggleOpts, **kwargs):
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393 dest = os.path.join('data', 'raw', trackData['label'] + '.bw')
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394 cmd = ['ln', data, dest]
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395 self.subprocess_check_call(cmd)
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396
3
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397 trackData.update({
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398 "urlTemplate": os.path.join('..', dest),
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399 "storeClass": "JBrowse/Store/SeqFeature/BigWig",
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400 "type": "JBrowse/View/Track/Wiggle/Density",
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401 })
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402
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403 trackData['type'] = wiggleOpts['type']
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404 trackData['variance_band'] = True if wiggleOpts['variance_band'] == 'true' else False
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405
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406 if 'min' in wiggleOpts and 'max' in wiggleOpts:
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407 trackData['min_score'] = wiggleOpts['min']
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408 trackData['max_score'] = wiggleOpts['max']
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409 else:
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410 trackData['autoscale'] = wiggleOpts.get('autoscale', 'local')
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411
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412 self._add_track_json(trackData)
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413
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414 def add_bam(self, data, trackData, bamOpts, bam_index=None, **kwargs):
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415 dest = os.path.join('data', 'raw', trackData['label'] + '.bam')
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416 cmd = ['ln', '-s', os.path.realpath(data), dest]
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417 self.subprocess_check_call(cmd)
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418
3
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419 cmd = ['ln', '-s', os.path.realpath(bam_index), dest + '.bai']
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420 self.subprocess_check_call(cmd)
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421
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422 trackData.update({
1
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423 "urlTemplate": os.path.join('..', dest),
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424 "type": "JBrowse/View/Track/Alignments2",
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425 "storeClass": "JBrowse/Store/SeqFeature/BAM",
3
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426 })
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427
1
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428
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429 self._add_track_json(trackData)
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430
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431 if bamOpts.get('auto_snp', 'false') == 'true':
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432 trackData2 = copy.copy(trackData)
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433 trackData2.update({
1
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434 "type": "JBrowse/View/Track/SNPCoverage",
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435 "key": trackData['key'] + " - SNPs/Coverage",
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436 "label": trackData['label'] + "_autosnp",
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437 })
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438 self._add_track_json(trackData2)
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439
3
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440 def add_vcf(self, data, trackData, vcfOpts={}, **kwargs):
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441 dest = os.path.join('data', 'raw', trackData['label'] + '.vcf')
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diff changeset
442 # ln?
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443 cmd = ['ln', '-s', data, dest]
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444 self.subprocess_check_call(cmd)
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445 cmd = ['bgzip', dest]
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446 self.subprocess_check_call(cmd)
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447 cmd = ['tabix', '-p', 'vcf', dest + '.gz']
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448 self.subprocess_check_call(cmd)
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449
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450 trackData.update({
1
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451 "urlTemplate": os.path.join('..', dest + '.gz'),
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452 "type": "JBrowse/View/Track/HTMLVariants",
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453 "storeClass": "JBrowse/Store/SeqFeature/VCFTabix",
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454 })
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455 self._add_track_json(trackData)
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456
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457 def add_features(self, data, format, trackData, gffOpts, **kwargs):
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458 cmd = [
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459 'perl', self._jbrowse_bin('flatfile-to-json.pl'),
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460 self.TN_TABLE.get(format, 'gff'),
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461 data,
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462 '--trackLabel', trackData['label'],
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463 # '--trackType', 'JBrowse/View/Track/CanvasFeatures',
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464 '--key', trackData['key']
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465 ]
1
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466
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467 config = copy.copy(trackData)
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468 clientConfig = trackData['style']
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469 del config['style']
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470
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471 if 'match' in gffOpts:
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472 config['glyph'] = 'JBrowse/View/FeatureGlyph/Segments'
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473 cmd += ['--type', gffOpts['match']]
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474
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475 cmd += ['--clientConfig', json.dumps(clientConfig),
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476 ]
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diff changeset
477
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478 if 'trackType' in gffOpts:
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479 cmd += [
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480 '--trackType', gffOpts['trackType']
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481 ]
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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482 else:
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483 cmd += [
3
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484 '--trackType', 'JBrowse/View/Track/CanvasFeatures'
5
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485 ]
1
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486
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487 cmd.extend(['--config', json.dumps(config)])
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488
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489 self.subprocess_check_call(cmd)
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490
3
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491
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492 def process_annotations(self, track):
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493 outputTrackConfig = {
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494 'style': {
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495 'label': track['style'].get('label', 'description'),
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496 'className': track['style'].get('className', 'feature'),
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497 'description': track['style'].get('description', ''),
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498 },
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499 'category': track['category'],
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500 }
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501
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502 for i, (dataset_path, dataset_ext, track_human_label) in enumerate(track['trackfiles']):
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diff changeset
503 log.info('Processing %s / %s', track['category'], track_human_label)
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504 outputTrackConfig['key'] = track_human_label
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diff changeset
505 hashData = [dataset_path, track_human_label, track['category']]
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diff changeset
506 outputTrackConfig['label'] = hashlib.md5('|'.join(hashData)).hexdigest() + '_%s' % i
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507
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diff changeset
508 # Colour parsing is complex due to different track types having
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509 # different colour options.
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diff changeset
510 colourOptions = self.cs.parse_colours(track['conf']['options'], track['format'], gff3=dataset_path)
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diff changeset
511 # This used to be done with a dict.update() call, however that wiped out any previous style settings...
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512 for key in colourOptions:
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diff changeset
513 if key == 'style':
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514 for subkey in colourOptions['style']:
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515 outputTrackConfig['style'][subkey] = colourOptions['style'][subkey]
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516 else:
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diff changeset
517 outputTrackConfig[key] = colourOptions[key]
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diff changeset
518
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519 # import pprint; pprint.pprint(track)
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520 # import sys; sys.exit()
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521 if dataset_ext in ('gff', 'gff3', 'bed'):
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522 self.add_features(dataset_path, dataset_ext, outputTrackConfig,
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523 track['conf']['options']['gff'])
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524 elif dataset_ext == 'bigwig':
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525 self.add_bigwig(dataset_path, outputTrackConfig,
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parents: 1
diff changeset
526 track['conf']['options']['wiggle'])
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parents: 1
diff changeset
527 elif dataset_ext == 'bam':
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528 real_indexes = track['conf']['options']['pileup']['bam_indices']['bam_index']
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529 if not isinstance(real_indexes, list):
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530 # <bam_indices>
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diff changeset
531 # <bam_index>/path/to/a.bam.bai</bam_index>
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diff changeset
532 # </bam_indices>
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533 #
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534 # The above will result in the 'bam_index' key containing a
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535 # string. If there are two or more indices, the container
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536 # becomes a list. Fun!
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537 real_indexes = [real_indexes]
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538
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539 self.add_bam(dataset_path, outputTrackConfig,
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parents: 1
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540 track['conf']['options']['pileup'],
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parents: 1
diff changeset
541 bam_index=real_indexes[i])
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diff changeset
542 elif dataset_ext == 'blastxml':
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543 self.add_blastxml(dataset_path, outputTrackConfig, track['conf']['options']['blast'])
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diff changeset
544 elif dataset_ext == 'vcf':
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
545 self.add_vcf(dataset_path, outputTrackConfig)
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parents: 0
diff changeset
546
5
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diff changeset
547 # Return non-human label for use in other fields
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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parents: 3
diff changeset
548 yield outputTrackConfig['label']
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parents: 3
diff changeset
549
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parents: 3
diff changeset
550 def add_final_data(self, data):
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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parents: 3
diff changeset
551 viz_data = {}
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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parents: 3
diff changeset
552 if len(data['visibility']['default_on']) > 0:
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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parents: 3
diff changeset
553 viz_data['defaultTracks'] = ','.join(data['visibility']['default_on'])
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
554
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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parents: 3
diff changeset
555 if len(data['visibility']['always']) > 0:
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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parents: 3
diff changeset
556 viz_data['alwaysOnTracks'] = ','.join(data['visibility']['always'])
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parents: 3
diff changeset
557
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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parents: 3
diff changeset
558 if len(data['visibility']['force']) > 0:
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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parents: 3
diff changeset
559 viz_data['forceTracks'] = ','.join(data['visibility']['force'])
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parents: 3
diff changeset
560
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parents: 3
diff changeset
561 generalData = {}
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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parents: 3
diff changeset
562 if data['general']['aboutDescription'] is not None:
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
563 generalData['aboutThisBrowser'] = {'description': data['general']['aboutDescription'].strip()}
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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parents: 3
diff changeset
564
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
565 generalData['view'] = {
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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parents: 3
diff changeset
566 'trackPadding': data['general']['trackPadding']
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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parents: 3
diff changeset
567 }
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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parents: 3
diff changeset
568 generalData['shareLink'] = (data['general']['shareLink'] == 'true')
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
569 generalData['show_tracklist'] = (data['general']['show_tracklist'] == 'true')
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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parents: 3
diff changeset
570 generalData['show_nav'] = (data['general']['show_nav'] == 'true')
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parents: 3
diff changeset
571 generalData['show_overview'] = (data['general']['show_overview'] == 'true')
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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parents: 3
diff changeset
572 generalData['show_menu'] = (data['general']['show_menu'] == 'true')
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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573 generalData['hideGenomeOptions'] = (data['general']['hideGenomeOptions'] == 'true')
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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574
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diff changeset
575 viz_data.update(generalData)
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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parents: 3
diff changeset
576 self._add_json(viz_data)
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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parents: 3
diff changeset
577
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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parents: 0
diff changeset
578 def clone_jbrowse(self, jbrowse_dir, destination):
3
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parents: 1
diff changeset
579 """Clone a JBrowse directory into a destination directory.
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parents: 1
diff changeset
580 """
1
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581 # JBrowse seems to have included some bad symlinks, cp ignores bad symlinks
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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parents: 0
diff changeset
582 # unlike copytree
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583 cmd = ['cp', '-r', os.path.join(jbrowse_dir, '.'), destination]
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parents: 1
diff changeset
584 log.debug(' '.join(cmd))
1
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585 subprocess.check_call(cmd)
3
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586 cmd = ['mkdir', '-p', os.path.join(destination, 'data', 'raw')]
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587 log.debug(' '.join(cmd))
1
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iuc
parents: 0
diff changeset
588 subprocess.check_call(cmd)
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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589
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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parents: 0
diff changeset
590 # http://unix.stackexchange.com/a/38691/22785
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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591 # JBrowse releases come with some broken symlinks
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
592 cmd = ['find', destination, '-type', 'l', '-xtype', 'l', '-exec', 'rm', "'{}'", '+']
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593 log.debug(' '.join(cmd))
1
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parents: 0
diff changeset
594 subprocess.check_call(cmd)
0
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diff changeset
595
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iuc
parents:
diff changeset
596
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
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diff changeset
597 if __name__ == '__main__':
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diff changeset
598 parser = argparse.ArgumentParser(description="", epilog="")
3
7342f467507b Uploaded v0.4 of JBrowse
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599 parser.add_argument('xml', type=file, help='Track Configuration')
0
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diff changeset
600
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
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diff changeset
601 parser.add_argument('--jbrowse', help='Folder containing a jbrowse release')
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
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602 parser.add_argument('--outdir', help='Output directory', default='out')
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diff changeset
603 parser.add_argument('--standalone', help='Standalone mode includes a copy of JBrowse', action='store_true')
0
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
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diff changeset
604 args = parser.parse_args()
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
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diff changeset
605
3
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diff changeset
606 tree = ET.parse(args.xml.name)
7342f467507b Uploaded v0.4 of JBrowse
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diff changeset
607 root = tree.getroot()
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parents: 1
diff changeset
608
1
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diff changeset
609 jc = JbrowseConnector(
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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diff changeset
610 jbrowse=args.jbrowse,
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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diff changeset
611 outdir=args.outdir,
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diff changeset
612 genomes=[os.path.realpath(x.text) for x in root.findall('metadata/genomes/genome')],
7342f467507b Uploaded v0.4 of JBrowse
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613 standalone=args.standalone,
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
614 gencode=root.find('metadata/gencode').text
1
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iuc
parents: 0
diff changeset
615 )
0
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff changeset
616
5
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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diff changeset
617 extra_data = {
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
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diff changeset
618 'visibility': {
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
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diff changeset
619 'default_on': [],
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
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diff changeset
620 'default_off': [],
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
621 'force': [],
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
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diff changeset
622 'always': [],
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
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diff changeset
623 },
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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624 'general': {
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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diff changeset
625 'defaultLocation': root.find('metadata/general/defaultLocation').text,
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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626 'trackPadding': int(root.find('metadata/general/trackPadding').text),
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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diff changeset
627 'shareLink': root.find('metadata/general/shareLink').text,
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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diff changeset
628 'aboutDescription': root.find('metadata/general/aboutDescription').text,
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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diff changeset
629 'show_tracklist': root.find('metadata/general/show_tracklist').text,
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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diff changeset
630 'show_nav': root.find('metadata/general/show_nav').text,
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
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diff changeset
631 'show_overview': root.find('metadata/general/show_overview').text,
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
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diff changeset
632 'show_menu': root.find('metadata/general/show_menu').text,
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
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633 'hideGenomeOptions': root.find('metadata/general/hideGenomeOptions').text,
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
634 }
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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diff changeset
635 }
3
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diff changeset
636 for track in root.findall('tracks/track'):
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diff changeset
637 track_conf = {}
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iuc
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diff changeset
638 track_conf['trackfiles'] = [
7342f467507b Uploaded v0.4 of JBrowse
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639 (os.path.realpath(x.attrib['path']), x.attrib['ext'], x.attrib['label'])
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diff changeset
640 for x in track.findall('files/trackFile')
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
641 ]
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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diff changeset
642
3
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iuc
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diff changeset
643 track_conf['category'] = track.attrib['cat']
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iuc
parents: 1
diff changeset
644 track_conf['format'] = track.attrib['format']
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
645 try:
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diff changeset
646 # Only pertains to gff3 + blastxml. TODO?
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diff changeset
647 track_conf['style'] = {t.tag: t.text for t in track.find('options/style')}
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iuc
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diff changeset
648 except TypeError, te:
7342f467507b Uploaded v0.4 of JBrowse
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diff changeset
649 track_conf['style'] = {}
7342f467507b Uploaded v0.4 of JBrowse
iuc
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diff changeset
650 pass
7342f467507b Uploaded v0.4 of JBrowse
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diff changeset
651 track_conf['conf'] = etree_to_dict(track.find('options'))
5
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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diff changeset
652 keys = jc.process_annotations(track_conf)
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
653
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
654
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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diff changeset
655 for key in keys:
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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diff changeset
656 extra_data['visibility'][track.attrib.get('visibility', 'default_off')].append(key)
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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diff changeset
657
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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diff changeset
658 jc.add_final_data(extra_data)