annotate jbrowse.py @ 23:dba3c47e1798 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit cf2c8f3039021b645ac45980a02ffe1f69a3f958
author iuc
date Wed, 12 Dec 2018 02:54:31 -0500
parents 5f70e7fe6077
children fa30df9b79c2
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1 #!/usr/bin/env python
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2 import argparse
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3 import binascii
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4 import copy
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5 import datetime
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6 import hashlib
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7 import json
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8 import logging
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9 import os
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10 import shutil
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11 import struct
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12 import subprocess
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13 import tempfile
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14 import xml.etree.ElementTree as ET
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15 from collections import defaultdict
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16
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17 from Bio.Data import CodonTable
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18 logging.basicConfig(level=logging.INFO)
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19 log = logging.getLogger('jbrowse')
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20 TODAY = datetime.datetime.now().strftime("%Y-%m-%d")
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21 GALAXY_INFRASTRUCTURE_URL = None
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23
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24 class ColorScaling(object):
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25
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26 COLOR_FUNCTION_TEMPLATE = """
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27 function(feature, variableName, glyphObject, track) {{
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28 var score = {score};
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29 {opacity}
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30 return 'rgba({red}, {green}, {blue}, ' + opacity + ')';
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31 }}
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32 """
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33
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34 COLOR_FUNCTION_TEMPLATE_QUAL = r"""
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35 function(feature, variableName, glyphObject, track) {{
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36 var search_up = function self(sf, attr){{
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37 if(sf.get(attr) !== undefined){{
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38 return sf.get(attr);
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39 }}
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40 if(sf.parent() === undefined) {{
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41 return;
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42 }}else{{
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43 return self(sf.parent(), attr);
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44 }}
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45 }};
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46
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47 var search_down = function self(sf, attr){{
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48 if(sf.get(attr) !== undefined){{
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49 return sf.get(attr);
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50 }}
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51 if(sf.children() === undefined) {{
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52 return;
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53 }}else{{
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54 var kids = sf.children();
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55 for(var child_idx in kids){{
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56 var x = self(kids[child_idx], attr);
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57 if(x !== undefined){{
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58 return x;
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59 }}
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60 }}
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61 return;
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62 }}
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63 }};
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64
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65 var color = ({user_spec_color} || search_up(feature, 'color') || search_down(feature, 'color') || {auto_gen_color});
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66 var score = (search_up(feature, 'score') || search_down(feature, 'score'));
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67 {opacity}
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68 if(score === undefined){{ opacity = 1; }}
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69 var result = /^#?([a-f\d]{{2}})([a-f\d]{{2}})([a-f\d]{{2}})$/i.exec(color);
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70 var red = parseInt(result[1], 16);
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71 var green = parseInt(result[2], 16);
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72 var blue = parseInt(result[3], 16);
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73 if(isNaN(opacity) || opacity < 0){{ opacity = 0; }}
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74 return 'rgba(' + red + ',' + green + ',' + blue + ',' + opacity + ')';
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75 }}
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76 """
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77
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78 OPACITY_MATH = {
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79 'linear': """
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80 var opacity = (score - ({min})) / (({max}) - ({min}));
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81 """,
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82 'logarithmic': """
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83 var opacity = (score - ({min})) / (({max}) - ({min}));
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84 opacity = Math.log10(opacity) + Math.log10({max});
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85 """,
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86 'blast': """
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87 var opacity = 0;
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88 if(score == 0.0) {{
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89 opacity = 1;
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90 }} else {{
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91 opacity = (20 - Math.log10(score)) / 180;
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92 }}
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93 """
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94 }
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95
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96 BREWER_COLOUR_IDX = 0
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97 BREWER_COLOUR_SCHEMES = [
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98 (166, 206, 227),
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99 (31, 120, 180),
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100 (178, 223, 138),
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101 (51, 160, 44),
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102 (251, 154, 153),
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103 (227, 26, 28),
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104 (253, 191, 111),
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105 (255, 127, 0),
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106 (202, 178, 214),
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107 (106, 61, 154),
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108 (255, 255, 153),
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109 (177, 89, 40),
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110 (228, 26, 28),
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111 (55, 126, 184),
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112 (77, 175, 74),
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113 (152, 78, 163),
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114 (255, 127, 0),
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115 ]
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116
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117 BREWER_DIVERGING_PALLETES = {
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118 'BrBg': ("#543005", "#003c30"),
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119 'PiYg': ("#8e0152", "#276419"),
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120 'PRGn': ("#40004b", "#00441b"),
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121 'PuOr': ("#7f3b08", "#2d004b"),
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122 'RdBu': ("#67001f", "#053061"),
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123 'RdGy': ("#67001f", "#1a1a1a"),
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124 'RdYlBu': ("#a50026", "#313695"),
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125 'RdYlGn': ("#a50026", "#006837"),
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126 'Spectral': ("#9e0142", "#5e4fa2"),
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127 }
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128
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129 def __init__(self):
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130 self.brewer_colour_idx = 0
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131
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132 def rgb_from_hex(self, hexstr):
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133 # http://stackoverflow.com/questions/4296249/how-do-i-convert-a-hex-triplet-to-an-rgb-tuple-and-back
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134 return struct.unpack('BBB', binascii.unhexlify(hexstr))
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135
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136 def min_max_gff(self, gff_file):
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137 min_val = None
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138 max_val = None
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139 with open(gff_file, 'r') as handle:
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140 for line in handle:
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141 try:
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142 value = float(line.split('\t')[5])
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143 min_val = min(value, (min_val or value))
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144 max_val = max(value, (max_val or value))
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145
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146 if value < min_val:
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147 min_val = value
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148
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149 if value > max_val:
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150 max_val = value
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151 except Exception:
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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152 pass
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153 return min_val, max_val
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154
3
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155 def hex_from_rgb(self, r, g, b):
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156 return '#%02x%02x%02x' % (r, g, b)
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157
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158 def _get_colours(self):
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159 r, g, b = self.BREWER_COLOUR_SCHEMES[self.brewer_colour_idx % len(self.BREWER_COLOUR_SCHEMES)]
3
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160 self.brewer_colour_idx += 1
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161 return r, g, b
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162
8
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163 def parse_menus(self, track):
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164 trackConfig = {'menuTemplate': [{}, {}, {}, {}]}
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165
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166 if 'menu' in track['menus']:
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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167 menu_list = [track['menus']['menu']]
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168 if isinstance(track['menus']['menu'], list):
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169 menu_list = track['menus']['menu']
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170
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171 for m in menu_list:
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172 tpl = {
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173 'action': m['action'],
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174 'label': m.get('label', '{name}'),
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175 'iconClass': m.get('iconClass', 'dijitIconBookmark'),
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176 }
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177 if 'url' in m:
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178 tpl['url'] = m['url']
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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179 if 'content' in m:
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180 tpl['content'] = m['content']
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181 if 'title' in m:
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182 tpl['title'] = m['title']
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183
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184 trackConfig['menuTemplate'].append(tpl)
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185
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186 return trackConfig
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187
3
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188 def parse_colours(self, track, trackFormat, gff3=None):
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189 # Wiggle tracks have a bicolor pallete
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190 trackConfig = {'style': {}}
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191 if trackFormat == 'wiggle':
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192
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193 trackConfig['style']['pos_color'] = track['wiggle']['color_pos']
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194 trackConfig['style']['neg_color'] = track['wiggle']['color_neg']
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195
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196 if trackConfig['style']['pos_color'] == '__auto__':
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197 trackConfig['style']['neg_color'] = self.hex_from_rgb(*self._get_colours())
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198 trackConfig['style']['pos_color'] = self.hex_from_rgb(*self._get_colours())
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199
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200 # Wiggle tracks can change colour at a specified place
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201 bc_pivot = track['wiggle']['bicolor_pivot']
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202 if bc_pivot not in ('mean', 'zero'):
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203 # The values are either one of those two strings
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204 # or a number
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205 bc_pivot = float(bc_pivot)
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206 trackConfig['bicolor_pivot'] = bc_pivot
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207 elif 'scaling' in track:
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208 if track['scaling']['method'] == 'ignore':
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209 if track['scaling']['scheme']['color'] != '__auto__':
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210 trackConfig['style']['color'] = track['scaling']['scheme']['color']
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211 else:
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212 trackConfig['style']['color'] = self.hex_from_rgb(*self._get_colours())
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213 else:
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214 # Scored method
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215 algo = track['scaling']['algo']
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216 # linear, logarithmic, blast
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217 scales = track['scaling']['scales']
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218 # type __auto__, manual (min, max)
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219 scheme = track['scaling']['scheme']
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220 # scheme -> (type (opacity), color)
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221 # ==================================
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222 # GENE CALLS OR BLAST
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223 # ==================================
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224 if trackFormat == 'blast':
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225 red, green, blue = self._get_colours()
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226 color_function = self.COLOR_FUNCTION_TEMPLATE.format(**{
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227 'score': "feature._parent.get('score')",
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228 'opacity': self.OPACITY_MATH['blast'],
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229 'red': red,
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230 'green': green,
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231 'blue': blue,
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232 })
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233 trackConfig['style']['color'] = color_function.replace('\n', '')
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234 elif trackFormat == 'gene_calls':
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235 # Default values, based on GFF3 spec
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236 min_val = 0
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237 max_val = 1000
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238 # Get min/max and build a scoring function since JBrowse doesn't
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239 if scales['type'] == 'automatic' or scales['type'] == '__auto__':
3
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240 min_val, max_val = self.min_max_gff(gff3)
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241 else:
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242 min_val = scales.get('min', 0)
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243 max_val = scales.get('max', 1000)
3
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244
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245 if scheme['color'] == '__auto__':
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246 user_color = 'undefined'
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247 auto_color = "'%s'" % self.hex_from_rgb(*self._get_colours())
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248 elif scheme['color'].startswith('#'):
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249 user_color = "'%s'" % self.hex_from_rgb(*self.rgb_from_hex(scheme['color'][1:]))
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250 auto_color = 'undefined'
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251 else:
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252 user_color = 'undefined'
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253 auto_color = "'%s'" % self.hex_from_rgb(*self._get_colours())
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254
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255 color_function = self.COLOR_FUNCTION_TEMPLATE_QUAL.format(**{
8
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256 'opacity': self.OPACITY_MATH[algo].format(**{'max': max_val, 'min': min_val}),
3
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257 'user_spec_color': user_color,
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258 'auto_gen_color': auto_color,
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259 })
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260
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261 trackConfig['style']['color'] = color_function.replace('\n', '')
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262 return trackConfig
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263
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264
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265 def etree_to_dict(t):
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266 d = {t.tag: {} if t.attrib else None}
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267 children = list(t)
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268 if children:
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269 dd = defaultdict(list)
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270 for dc in map(etree_to_dict, children):
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271 for k, v in dc.items():
3
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272 dd[k].append(v)
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273 d = {t.tag: {k: v[0] if len(v) == 1 else v for k, v in dd.items()}}
3
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274 if t.attrib:
10
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275 d[t.tag].update(('@' + k, v) for k, v in t.attrib.items())
3
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276 if t.text:
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277 text = t.text.strip()
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278 if children or t.attrib:
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279 if text:
8
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280 d[t.tag]['#text'] = text
3
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281 else:
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282 d[t.tag] = text
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283 return d
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284
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285
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286 # score comes from feature._parent.get('score') or feature.get('score')
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287
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288 INSTALLED_TO = os.path.dirname(os.path.realpath(__file__))
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289
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290
17
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291 def metadata_from_node(node):
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292 metadata = {}
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293 try:
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294 if len(node.findall('dataset')) != 1:
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295 # exit early
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296 return metadata
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297 except Exception:
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298 return {}
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299
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300 for (key, value) in node.findall('dataset')[0].attrib.items():
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301 metadata['dataset_%s' % key] = value
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302
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303 for (key, value) in node.findall('history')[0].attrib.items():
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304 metadata['history_%s' % key] = value
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305
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306 for (key, value) in node.findall('metadata')[0].attrib.items():
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307 metadata['metadata_%s' % key] = value
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308
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309 for (key, value) in node.findall('tool')[0].attrib.items():
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310 metadata['tool_%s' % key] = value
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311
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312 # Additional Mappings applied:
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313 metadata['dataset_edam_format'] = '<a target="_blank" href="http://edamontology.org/{0}">{1}</a>'.format(metadata['dataset_edam_format'], metadata['dataset_file_ext'])
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314 metadata['history_user_email'] = '<a href="mailto:{0}">{0}</a>'.format(metadata['history_user_email'])
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315 metadata['history_display_name'] = '<a target="_blank" href="{galaxy}/history/view/{encoded_hist_id}">{hist_name}</a>'.format(
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316 galaxy=GALAXY_INFRASTRUCTURE_URL,
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317 encoded_hist_id=metadata['history_id'],
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318 hist_name=metadata['history_display_name']
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319 )
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320 metadata['tool_tool'] = '<a target="_blank" href="{galaxy}/datasets/{encoded_id}/show_params">{tool_id}</a>'.format(
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321 galaxy=GALAXY_INFRASTRUCTURE_URL,
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322 encoded_id=metadata['dataset_id'],
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323 tool_id=metadata['tool_tool_id'],
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324 tool_version=metadata['tool_tool_version'],
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325 )
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326 return metadata
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327
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328
3
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parents: 1
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329 class JbrowseConnector(object):
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330
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331 def __init__(self, jbrowse, outdir, genomes, standalone=False, gencode=1):
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332 self.TN_TABLE = {
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333 'gff3': '--gff',
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334 'gff': '--gff',
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335 'bed': '--bed',
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336 'genbank': '--gbk',
1
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parents: 0
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337 }
3
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338
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339 self.cs = ColorScaling()
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parents: 1
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340 self.jbrowse = jbrowse
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parents: 1
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341 self.outdir = outdir
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342 self.genome_paths = genomes
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343 self.standalone = standalone
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344 self.gencode = gencode
8
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345 self.tracksToIndex = []
3
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parents: 1
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346
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347 if standalone:
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348 self.clone_jbrowse(self.jbrowse, self.outdir)
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349 else:
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350 try:
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351 os.makedirs(self.outdir)
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parents: 1
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352 except OSError:
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parents: 1
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353 # Ignore if the folder exists
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parents: 1
diff changeset
354 pass
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diff changeset
355
17
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356 try:
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357 os.makedirs(os.path.join(self.outdir, 'data', 'raw'))
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358 except OSError:
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359 # Ignore if the folder exists
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iuc
parents: 16
diff changeset
360 pass
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361
3
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362 self.process_genomes()
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363 self.update_gencode()
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364
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diff changeset
365 def update_gencode(self):
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366 table = CodonTable.unambiguous_dna_by_id[int(self.gencode)]
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367 trackList = os.path.join(self.outdir, 'data', 'trackList.json')
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368 with open(trackList, 'r') as handle:
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369 trackListData = json.load(handle)
1
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370
3
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parents: 1
diff changeset
371 trackListData['tracks'][0].update({
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parents: 1
diff changeset
372 'codonStarts': table.start_codons,
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iuc
parents: 1
diff changeset
373 'codonStops': table.stop_codons,
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parents: 1
diff changeset
374 'codonTable': table.forward_table,
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parents: 1
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375 })
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parents: 1
diff changeset
376
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parents: 1
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377 with open(trackList, 'w') as handle:
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parents: 1
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378 json.dump(trackListData, handle, indent=2)
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parents: 1
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379
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parents: 1
diff changeset
380 def subprocess_check_call(self, command):
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parents: 1
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381 log.debug('cd %s && %s', self.outdir, ' '.join(command))
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parents: 1
diff changeset
382 subprocess.check_call(command, cwd=self.outdir)
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parents: 1
diff changeset
383
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parents: 1
diff changeset
384 def _jbrowse_bin(self, command):
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parents: 1
diff changeset
385 return os.path.realpath(os.path.join(self.jbrowse, 'bin', command))
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parents: 1
diff changeset
386
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parents: 1
diff changeset
387 def process_genomes(self):
17
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parents: 16
diff changeset
388 for genome_node in self.genome_paths:
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parents: 16
diff changeset
389 # TODO: Waiting on https://github.com/GMOD/jbrowse/pull/884
3
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parents: 1
diff changeset
390 self.subprocess_check_call([
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parents: 1
diff changeset
391 'perl', self._jbrowse_bin('prepare-refseqs.pl'),
17
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parents: 16
diff changeset
392 '--fasta', genome_node['path']])
3
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iuc
parents: 1
diff changeset
393
8
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parents: 5
diff changeset
394 def generate_names(self):
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diff changeset
395 # Generate names
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diff changeset
396 args = [
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parents: 5
diff changeset
397 'perl', self._jbrowse_bin('generate-names.pl'),
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398 '--hashBits', '16'
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399 ]
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parents: 5
diff changeset
400
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401 tracks = ','.join(self.tracksToIndex)
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402 if tracks:
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403 args += ['--tracks', tracks]
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404 else:
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405 # No tracks to index, index only the refseq
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406 args += ['--tracks', 'DNA']
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407
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408 self.subprocess_check_call(args)
3
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409
5
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410 def _add_json(self, json_data):
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411 cmd = [
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412 'perl', self._jbrowse_bin('add-json.pl'),
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413 json.dumps(json_data),
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414 os.path.join('data', 'trackList.json')
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415 ]
3
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416 self.subprocess_check_call(cmd)
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417
3
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418 def _add_track_json(self, json_data):
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419 if len(json_data) == 0:
3
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420 return
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421
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422 tmp = tempfile.NamedTemporaryFile(delete=False)
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423 tmp.write(json.dumps(json_data))
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424 tmp.close()
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425 cmd = ['perl', self._jbrowse_bin('add-track-json.pl'), tmp.name,
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426 os.path.join('data', 'trackList.json')]
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427 self.subprocess_check_call(cmd)
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428 os.unlink(tmp.name)
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429
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430 def _blastxml_to_gff3(self, xml, min_gap=10):
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431 gff3_unrebased = tempfile.NamedTemporaryFile(delete=False)
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432 cmd = ['python', os.path.join(INSTALLED_TO, 'blastxml_to_gapped_gff3.py'),
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433 '--trim', '--trim_end', '--min_gap', str(min_gap), xml]
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434 log.debug('cd %s && %s > %s', self.outdir, ' '.join(cmd), gff3_unrebased.name)
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435 subprocess.check_call(cmd, cwd=self.outdir, stdout=gff3_unrebased)
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436 gff3_unrebased.close()
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437 return gff3_unrebased.name
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438
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439 def add_blastxml(self, data, trackData, blastOpts, **kwargs):
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440 gff3 = self._blastxml_to_gff3(data, min_gap=blastOpts['min_gap'])
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441
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442 if 'parent' in blastOpts and blastOpts['parent'] != 'None':
3
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443 gff3_rebased = tempfile.NamedTemporaryFile(delete=False)
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444 cmd = ['python', os.path.join(INSTALLED_TO, 'gff3_rebase.py')]
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445 if blastOpts.get('protein', 'false') == 'true':
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446 cmd.append('--protein2dna')
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447 cmd.extend([os.path.realpath(blastOpts['parent']), gff3])
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448 log.debug('cd %s && %s > %s', self.outdir, ' '.join(cmd), gff3_rebased.name)
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449 subprocess.check_call(cmd, cwd=self.outdir, stdout=gff3_rebased)
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450 gff3_rebased.close()
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451
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452 # Replace original gff3 file
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453 shutil.copy(gff3_rebased.name, gff3)
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454 os.unlink(gff3_rebased.name)
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455
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456 config = {
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457 'glyph': 'JBrowse/View/FeatureGlyph/Segments',
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458 "category": trackData['category'],
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459 }
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460
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461 clientConfig = trackData['style']
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462
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463 cmd = ['perl', self._jbrowse_bin('flatfile-to-json.pl'),
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464 '--gff', gff3,
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465 '--trackLabel', trackData['label'],
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466 '--key', trackData['key'],
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467 '--clientConfig', json.dumps(clientConfig),
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468 '--config', json.dumps(config),
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469 '--trackType', 'BlastView/View/Track/CanvasFeatures'
3
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470 ]
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471
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diff changeset
472 # className in --clientConfig is ignored, it needs to be set with --className
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473 if 'className' in trackData['style']:
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474 cmd += ['--className', trackData['style']['className']]
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475
3
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476 self.subprocess_check_call(cmd)
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parents: 1
diff changeset
477 os.unlink(gff3)
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diff changeset
478
8
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diff changeset
479 if blastOpts.get('index', 'false') == 'true':
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diff changeset
480 self.tracksToIndex.append("%s" % trackData['label'])
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481
3
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482 def add_bigwig(self, data, trackData, wiggleOpts, **kwargs):
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483 dest = os.path.join('data', 'raw', trackData['label'] + '.bw')
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diff changeset
484 cmd = ['ln', '-s', data, dest]
1
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parents: 0
diff changeset
485 self.subprocess_check_call(cmd)
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parents: 0
diff changeset
486
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diff changeset
487 url = os.path.join('raw', trackData['label'] + '.bw')
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488 trackData.update({
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489 "urlTemplate": url,
3
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490 "storeClass": "JBrowse/Store/SeqFeature/BigWig",
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parents: 1
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491 "type": "JBrowse/View/Track/Wiggle/Density",
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492 })
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493
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494 trackData['type'] = wiggleOpts['type']
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parents: 1
diff changeset
495 trackData['variance_band'] = True if wiggleOpts['variance_band'] == 'true' else False
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parents: 1
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496
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diff changeset
497 if 'min' in wiggleOpts and 'max' in wiggleOpts:
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parents: 1
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498 trackData['min_score'] = wiggleOpts['min']
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parents: 1
diff changeset
499 trackData['max_score'] = wiggleOpts['max']
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parents: 1
diff changeset
500 else:
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parents: 1
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501 trackData['autoscale'] = wiggleOpts.get('autoscale', 'local')
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parents: 1
diff changeset
502
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parents: 16
diff changeset
503 trackData['scale'] = wiggleOpts['scale']
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diff changeset
504
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505 self._add_track_json(trackData)
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parents: 1
diff changeset
506
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diff changeset
507 def add_bam(self, data, trackData, bamOpts, bam_index=None, **kwargs):
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508 dest = os.path.join('data', 'raw', trackData['label'] + '.bam')
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parents: 1
diff changeset
509 cmd = ['ln', '-s', os.path.realpath(data), dest]
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parents: 0
diff changeset
510 self.subprocess_check_call(cmd)
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parents: 0
diff changeset
511
3
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parents: 1
diff changeset
512 cmd = ['ln', '-s', os.path.realpath(bam_index), dest + '.bai']
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diff changeset
513 self.subprocess_check_call(cmd)
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parents: 1
diff changeset
514
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diff changeset
515 url = os.path.join('raw', trackData['label'] + '.bam')
3
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parents: 1
diff changeset
516 trackData.update({
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parents: 11
diff changeset
517 "urlTemplate": url,
1
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parents: 0
diff changeset
518 "type": "JBrowse/View/Track/Alignments2",
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diff changeset
519 "storeClass": "JBrowse/Store/SeqFeature/BAM",
3
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parents: 1
diff changeset
520 })
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parents: 1
diff changeset
521
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parents: 13
diff changeset
522 # Apollo will only switch to the (prettier) 'bam-read' className if it's not set explicitly in the track config
18be2d72fdee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
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parents: 13
diff changeset
523 # So remove the default 'feature' value for these bam tracks
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parents: 13
diff changeset
524 if 'className' in trackData['style'] and trackData['style']['className'] == 'feature':
18be2d72fdee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
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diff changeset
525 del trackData['style']['className']
18be2d72fdee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 13
diff changeset
526
3
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iuc
parents: 1
diff changeset
527 self._add_track_json(trackData)
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
528
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iuc
parents: 1
diff changeset
529 if bamOpts.get('auto_snp', 'false') == 'true':
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
530 trackData2 = copy.copy(trackData)
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
531 trackData2.update({
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
532 "type": "JBrowse/View/Track/SNPCoverage",
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
533 "key": trackData['key'] + " - SNPs/Coverage",
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 5
diff changeset
534 "label": trackData['label'] + "_autosnp",
3
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iuc
parents: 1
diff changeset
535 })
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iuc
parents: 1
diff changeset
536 self._add_track_json(trackData2)
1
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iuc
parents: 0
diff changeset
537
3
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parents: 1
diff changeset
538 def add_vcf(self, data, trackData, vcfOpts={}, **kwargs):
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parents: 1
diff changeset
539 dest = os.path.join('data', 'raw', trackData['label'] + '.vcf')
1
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iuc
parents: 0
diff changeset
540 # ln?
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
541 cmd = ['ln', '-s', data, dest]
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
542 self.subprocess_check_call(cmd)
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
543 cmd = ['bgzip', dest]
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
544 self.subprocess_check_call(cmd)
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
545 cmd = ['tabix', '-p', 'vcf', dest + '.gz']
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
546 self.subprocess_check_call(cmd)
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
547
12
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iuc
parents: 11
diff changeset
548 url = os.path.join('raw', trackData['label'] + '.vcf')
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iuc
parents: 1
diff changeset
549 trackData.update({
12
db5fe5a3176a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 11
diff changeset
550 "urlTemplate": url,
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
551 "type": "JBrowse/View/Track/HTMLVariants",
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
552 "storeClass": "JBrowse/Store/SeqFeature/VCFTabix",
3
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iuc
parents: 1
diff changeset
553 })
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
554 self._add_track_json(trackData)
1
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iuc
parents: 0
diff changeset
555
17
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parents: 16
diff changeset
556 def add_features(self, data, format, trackData, gffOpts, metadata=None, **kwargs):
3
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iuc
parents: 1
diff changeset
557 cmd = [
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
558 'perl', self._jbrowse_bin('flatfile-to-json.pl'),
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
559 self.TN_TABLE.get(format, 'gff'),
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iuc
parents: 1
diff changeset
560 data,
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
561 '--trackLabel', trackData['label'],
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
562 '--key', trackData['key']
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
563 ]
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
564
13
69c5e9c0add0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit bb4fe9cc4bc03918afa525569ed36144a819ce79
iuc
parents: 12
diff changeset
565 # className in --clientConfig is ignored, it needs to be set with --className
69c5e9c0add0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit bb4fe9cc4bc03918afa525569ed36144a819ce79
iuc
parents: 12
diff changeset
566 if 'className' in trackData['style']:
69c5e9c0add0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit bb4fe9cc4bc03918afa525569ed36144a819ce79
iuc
parents: 12
diff changeset
567 cmd += ['--className', trackData['style']['className']]
69c5e9c0add0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit bb4fe9cc4bc03918afa525569ed36144a819ce79
iuc
parents: 12
diff changeset
568
3
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parents: 1
diff changeset
569 config = copy.copy(trackData)
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
570 clientConfig = trackData['style']
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
571 del config['style']
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
572
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 5
diff changeset
573 if 'match' in gffOpts:
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
574 config['glyph'] = 'JBrowse/View/FeatureGlyph/Segments'
21
1c718d8b3532 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9cac72c004cc7ef57be997e2fdafb3b1839a300f
iuc
parents: 20
diff changeset
575 if bool(gffOpts['match']):
1c718d8b3532 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9cac72c004cc7ef57be997e2fdafb3b1839a300f
iuc
parents: 20
diff changeset
576 # Can be empty for CanvasFeatures = will take all by default
1c718d8b3532 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9cac72c004cc7ef57be997e2fdafb3b1839a300f
iuc
parents: 20
diff changeset
577 cmd += ['--type', gffOpts['match']]
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
578
3
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parents: 1
diff changeset
579 cmd += ['--clientConfig', json.dumps(clientConfig),
5
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iuc
parents: 3
diff changeset
580 ]
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
581
10
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
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parents: 8
diff changeset
582 trackType = 'JBrowse/View/Track/CanvasFeatures'
5
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
583 if 'trackType' in gffOpts:
10
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
584 trackType = gffOpts['trackType']
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
585
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
586 if trackType == 'JBrowse/View/Track/CanvasFeatures':
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
587 if 'transcriptType' in gffOpts and gffOpts['transcriptType']:
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
588 config['transcriptType'] = gffOpts['transcriptType']
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
589 if 'subParts' in gffOpts and gffOpts['subParts']:
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
590 config['subParts'] = gffOpts['subParts']
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
591 if 'impliedUTRs' in gffOpts and gffOpts['impliedUTRs']:
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
592 config['impliedUTRs'] = gffOpts['impliedUTRs']
13
69c5e9c0add0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit bb4fe9cc4bc03918afa525569ed36144a819ce79
iuc
parents: 12
diff changeset
593 elif trackType == 'JBrowse/View/Track/HTMLFeatures':
69c5e9c0add0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit bb4fe9cc4bc03918afa525569ed36144a819ce79
iuc
parents: 12
diff changeset
594 if 'transcriptType' in gffOpts and gffOpts['transcriptType']:
69c5e9c0add0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit bb4fe9cc4bc03918afa525569ed36144a819ce79
iuc
parents: 12
diff changeset
595 cmd += ['--type', gffOpts['transcriptType']]
10
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
596
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
597 cmd += [
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
598 '--trackType', gffOpts['trackType']
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
599 ]
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
600
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
601 if metadata:
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
602 config.update({'metadata': metadata})
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
603 cmd.extend(['--config', json.dumps(config)])
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
604
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
605 self.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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parents: 0
diff changeset
606
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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parents: 5
diff changeset
607 if gffOpts.get('index', 'false') == 'true':
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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parents: 5
diff changeset
608 self.tracksToIndex.append("%s" % trackData['label'])
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parents: 1
diff changeset
609
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
610 def add_rest(self, url, trackData):
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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parents: 16
diff changeset
611 data = {
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
612 "label": trackData['label'],
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
613 "key": trackData['key'],
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
614 "category": trackData['category'],
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
615 "type": "JBrowse/View/Track/HTMLFeatures",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
616 "storeClass": "JBrowse/Store/SeqFeature/REST",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
617 "baseUrl": url,
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iuc
parents: 16
diff changeset
618 "query": {
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
619 "organism": "tyrannosaurus"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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parents: 16
diff changeset
620 }
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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parents: 16
diff changeset
621 }
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
622 self._add_track_json(data)
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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parents: 16
diff changeset
623
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iuc
parents: 1
diff changeset
624 def process_annotations(self, track):
17
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diff changeset
625 category = track['category'].replace('__pd__date__pd__', TODAY)
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parents: 1
diff changeset
626 outputTrackConfig = {
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627 'style': {
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628 'label': track['style'].get('label', 'description'),
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629 'className': track['style'].get('className', 'feature'),
3
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630 'description': track['style'].get('description', ''),
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diff changeset
631 },
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632 'overridePlugins': track['style'].get('overridePlugins', False) == 'True',
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633 'overrideDraggable': track['style'].get('overrideDraggable', False) == 'True',
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634 'maxHeight': track['style'].get('maxHeight', '600'),
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635 'category': category,
3
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parents: 1
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636 }
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637
16
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diff changeset
638 mapped_chars = {
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639 '>': '__gt__',
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diff changeset
640 '<': '__lt__',
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641 "'": '__sq__',
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642 '"': '__dq__',
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643 '[': '__ob__',
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644 ']': '__cb__',
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645 '{': '__oc__',
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646 '}': '__cc__',
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647 '@': '__at__',
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diff changeset
648 '#': '__pd__'
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649 }
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650
17
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diff changeset
651 for i, (dataset_path, dataset_ext, track_human_label, extra_metadata) in enumerate(track['trackfiles']):
16
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diff changeset
652 # Unsanitize labels (element_identifiers are always sanitized by Galaxy)
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653 for key, value in mapped_chars.items():
b5c5470d7c09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5
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diff changeset
654 track_human_label = track_human_label.replace(value, key)
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655
17
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656 log.info('Processing %s / %s', category, track_human_label)
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diff changeset
657 outputTrackConfig['key'] = track_human_label
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diff changeset
658 # We add extra data to hash for the case of REST + SPARQL.
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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diff changeset
659 try:
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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660 rest_url = track['conf']['options']['url']
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diff changeset
661 except KeyError:
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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diff changeset
662 rest_url = ''
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diff changeset
663
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parents: 16
diff changeset
664 # I chose to use track['category'] instead of 'category' here. This
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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diff changeset
665 # is intentional. This way re-running the tool on a different date
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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666 # will not generate different hashes and make comparison of outputs
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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diff changeset
667 # much simpler.
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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diff changeset
668 hashData = [dataset_path, track_human_label, track['category'], rest_url]
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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diff changeset
669 hashData = '|'.join(hashData).encode('utf-8')
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diff changeset
670 outputTrackConfig['label'] = hashlib.md5(hashData).hexdigest() + '_%s' % i
3
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671
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672 # Colour parsing is complex due to different track types having
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673 # different colour options.
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diff changeset
674 colourOptions = self.cs.parse_colours(track['conf']['options'], track['format'], gff3=dataset_path)
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diff changeset
675 # This used to be done with a dict.update() call, however that wiped out any previous style settings...
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676 for key in colourOptions:
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diff changeset
677 if key == 'style':
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678 for subkey in colourOptions['style']:
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679 outputTrackConfig['style'][subkey] = colourOptions['style'][subkey]
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680 else:
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681 outputTrackConfig[key] = colourOptions[key]
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diff changeset
682
12
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683 if 'menus' in track['conf']['options']:
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diff changeset
684 menus = self.cs.parse_menus(track['conf']['options'])
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diff changeset
685 outputTrackConfig.update(menus)
8
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parents: 5
diff changeset
686
5
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diff changeset
687 # import pprint; pprint.pprint(track)
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diff changeset
688 # import sys; sys.exit()
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parents: 1
diff changeset
689 if dataset_ext in ('gff', 'gff3', 'bed'):
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diff changeset
690 self.add_features(dataset_path, dataset_ext, outputTrackConfig,
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diff changeset
691 track['conf']['options']['gff'], metadata=extra_metadata)
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692 elif dataset_ext == 'bigwig':
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diff changeset
693 self.add_bigwig(dataset_path, outputTrackConfig,
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diff changeset
694 track['conf']['options']['wiggle'], metadata=extra_metadata)
3
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parents: 1
diff changeset
695 elif dataset_ext == 'bam':
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parents: 1
diff changeset
696 real_indexes = track['conf']['options']['pileup']['bam_indices']['bam_index']
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diff changeset
697 if not isinstance(real_indexes, list):
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parents: 1
diff changeset
698 # <bam_indices>
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diff changeset
699 # <bam_index>/path/to/a.bam.bai</bam_index>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
700 # </bam_indices>
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parents: 1
diff changeset
701 #
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
702 # The above will result in the 'bam_index' key containing a
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
703 # string. If there are two or more indices, the container
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
704 # becomes a list. Fun!
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parents: 1
diff changeset
705 real_indexes = [real_indexes]
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parents: 1
diff changeset
706
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parents: 1
diff changeset
707 self.add_bam(dataset_path, outputTrackConfig,
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
708 track['conf']['options']['pileup'],
17
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diff changeset
709 bam_index=real_indexes[i], metadata=extra_metadata)
3
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parents: 1
diff changeset
710 elif dataset_ext == 'blastxml':
17
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parents: 16
diff changeset
711 self.add_blastxml(dataset_path, outputTrackConfig, track['conf']['options']['blast'], metadata=extra_metadata)
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parents: 1
diff changeset
712 elif dataset_ext == 'vcf':
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parents: 16
diff changeset
713 self.add_vcf(dataset_path, outputTrackConfig, metadata=extra_metadata)
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parents: 16
diff changeset
714 elif dataset_ext == 'rest':
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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parents: 16
diff changeset
715 self.add_rest(track['conf']['options']['url'], outputTrackConfig, metadata=extra_metadata)
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parents: 16
diff changeset
716 else:
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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diff changeset
717 log.warn('Do not know how to handle %s', dataset_ext)
1
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parents: 0
diff changeset
718
5
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iuc
parents: 3
diff changeset
719 # 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
iuc
parents: 3
diff changeset
720 yield outputTrackConfig['label']
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
721
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iuc
parents: 3
diff changeset
722 def add_final_data(self, data):
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
723 viz_data = {}
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
724 if len(data['visibility']['default_on']) > 0:
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
725 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
726
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
727 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
728 viz_data['alwaysOnTracks'] = ','.join(data['visibility']['always'])
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
729
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iuc
parents: 3
diff changeset
730 if len(data['visibility']['force']) > 0:
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
731 viz_data['forceTracks'] = ','.join(data['visibility']['force'])
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
732
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
733 generalData = {}
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
734 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
735 generalData['aboutThisBrowser'] = {'description': data['general']['aboutDescription'].strip()}
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
736
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
737 generalData['view'] = {
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
738 'trackPadding': data['general']['trackPadding']
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
739 }
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
740 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
741 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
iuc
parents: 3
diff changeset
742 generalData['show_nav'] = (data['general']['show_nav'] == 'true')
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
743 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
iuc
parents: 3
diff changeset
744 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
iuc
parents: 3
diff changeset
745 generalData['hideGenomeOptions'] = (data['general']['hideGenomeOptions'] == 'true')
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
746 generalData['plugins'] = data['plugins']
5
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
747
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
748 viz_data.update(generalData)
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
749 self._add_json(viz_data)
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
750
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
751 if 'GCContent' in data['plugins_python']:
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
752 self._add_track_json({
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
753 "storeClass": "JBrowse/Store/SeqFeature/SequenceChunks",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
754 "type": "GCContent/View/Track/GCContentXY",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
755 "label": "GCContentXY",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
756 "urlTemplate": "seq/{refseq_dirpath}/{refseq}-",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
757 "bicolor_pivot": 0.5
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
758 # TODO: Expose params for everyone.
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
759 })
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
760
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
761 if 'ComboTrackSelector' in data['plugins_python']:
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
762 with open(os.path.join(self.outdir, 'data', 'trackList.json'), 'r') as handle:
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
763 trackListJson = json.load(handle)
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
764 trackListJson.update({
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
765 "trackSelector": {
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
766 "renameFacets": {
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
767 "tool_tool": "Tool ID",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
768 "tool_tool_id": "Tool ID",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
769 "tool_tool_version": "Tool Version",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
770 "dataset_edam_format": "EDAM",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
771 "dataset_size": "Size",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
772 "history_display_name": "History Name",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
773 "history_user_email": "Owner",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
774 "metadata_dbkey": "Dbkey",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
775 },
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
776 "displayColumns": [
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
777 "key",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
778 "tool_tool",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
779 "tool_tool_version",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
780 "dataset_edam_format",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
781 "dataset_size",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
782 "history_display_name",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
783 "history_user_email",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
784 "metadata_dbkey",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
785 ],
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
786 "type": "Faceted",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
787 "title": ["Galaxy Metadata"],
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
788 "escapeHTMLInData": False
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
789 },
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
790 "trackMetadata": {
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
791 "indexFacets": [
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
792 "category",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
793 "key",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
794 "tool_tool_id",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
795 "tool_tool_version",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
796 "dataset_edam_format",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
797 "history_user_email",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
798 "history_display_name"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
799 ]
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
800 }
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
801 })
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
802 with open(os.path.join(self.outdir, 'data', 'trackList2.json'), 'w') as handle:
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
803 json.dump(trackListJson, handle)
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
804
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
805 def clone_jbrowse(self, jbrowse_dir, destination):
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
806 """Clone a JBrowse directory into a destination directory.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
807 """
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
808 # 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
iuc
parents: 0
diff changeset
809 # unlike copytree
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
810 cmd = ['cp', '-r', os.path.join(jbrowse_dir, '.'), destination]
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
811 log.debug(' '.join(cmd))
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
812 subprocess.check_call(cmd)
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
813 cmd = ['mkdir', '-p', os.path.join(destination, 'data', 'raw')]
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
814 log.debug(' '.join(cmd))
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
815 subprocess.check_call(cmd)
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
816
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
817 # http://unix.stackexchange.com/a/38691/22785
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
818 # JBrowse releases come with some broken symlinks
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
819 cmd = ['find', destination, '-type', 'l', '-xtype', 'l']
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
820 log.debug(' '.join(cmd))
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
821 symlinks = subprocess.check_output(cmd)
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
822 for i in symlinks:
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
823 try:
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
824 os.unlink(i)
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
825 except OSError:
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
826 pass
0
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff changeset
827
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff changeset
828
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff changeset
829 if __name__ == '__main__':
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff changeset
830 parser = argparse.ArgumentParser(description="", epilog="")
10
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
831 parser.add_argument('xml', type=argparse.FileType('r'), help='Track Configuration')
0
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff changeset
832
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff changeset
833 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
iuc
parents:
diff changeset
834 parser.add_argument('--outdir', help='Output directory', default='out')
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
835 parser.add_argument('--standalone', help='Standalone mode includes a copy of JBrowse', action='store_true')
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
836 parser.add_argument('--version', '-V', action='version', version="%(prog)s 0.7.0")
0
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff changeset
837 args = parser.parse_args()
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff changeset
838
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
839 tree = ET.parse(args.xml.name)
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
840 root = tree.getroot()
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
841
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
842 jc = JbrowseConnector(
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
843 jbrowse=args.jbrowse,
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
844 outdir=args.outdir,
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
845 genomes=[
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
846 {
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
847 'path': os.path.realpath(x.attrib['path']),
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
848 'meta': metadata_from_node(x.find('metadata'))
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
849 }
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
850 for x in root.findall('metadata/genomes/genome')
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
851 ],
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
852 standalone=args.standalone,
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
853 gencode=root.find('metadata/gencode').text
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
854 )
0
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff changeset
855
5
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
856 extra_data = {
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
857 'visibility': {
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
858 'default_on': [],
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
859 'default_off': [],
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
860 'force': [],
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
861 'always': [],
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
862 },
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
863 'general': {
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
864 'defaultLocation': root.find('metadata/general/defaultLocation').text,
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
865 '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
iuc
parents: 3
diff changeset
866 'shareLink': root.find('metadata/general/shareLink').text,
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
867 'aboutDescription': root.find('metadata/general/aboutDescription').text,
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
868 '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
iuc
parents: 3
diff changeset
869 '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
parents: 3
diff changeset
870 '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
parents: 3
diff changeset
871 '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
parents: 3
diff changeset
872 'hideGenomeOptions': root.find('metadata/general/hideGenomeOptions').text,
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
873 },
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
874 'plugins': [{
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
875 'location': 'https://cdn.rawgit.com/TAMU-CPT/blastview/97572a21b7f011c2b4d9a0b5af40e292d694cbef/',
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
876 'name': 'BlastView'
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
877 }],
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
878 'plugins_python': ['BlastView'],
5
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
879 }
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
880
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
881 plugins = root.find('plugins').attrib
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
882 if plugins['GCContent'] == 'True':
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
883 extra_data['plugins_python'].append('GCContent')
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
884 extra_data['plugins'].append({
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
885 'location': 'https://cdn.rawgit.com/elsiklab/gccontent/5c8b0582ecebf9edf684c76af8075fb3d30ec3fa/',
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
886 'name': 'GCContent'
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
887 })
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
888
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
889 if plugins['Bookmarks'] == 'True':
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
890 extra_data['plugins'].append({
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
891 'location': 'https://cdn.rawgit.com/TAMU-CPT/bookmarks-jbrowse/5242694120274c86e1ccd5cb0e5e943e78f82393/',
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
892 'name': 'Bookmarks'
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
893 })
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
894
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
895 if plugins['ComboTrackSelector'] == 'True':
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
896 extra_data['plugins_python'].append('ComboTrackSelector')
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
897 extra_data['plugins'].append({
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
898 'location': 'https://cdn.rawgit.com/Arabidopsis-Information-Portal/ComboTrackSelector/52403928d5ccbe2e3a86b0fa5eb8e61c0f2e2f57',
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
899 'icon': 'https://galaxyproject.org/images/logos/galaxy-icon-square.png',
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
900 'name': 'ComboTrackSelector'
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
901 })
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
902
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
903 if plugins['theme'] == 'Minimalist':
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
904 extra_data['plugins'].append({
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
905 'location': 'https://cdn.rawgit.com/erasche/jbrowse-minimalist-theme/d698718442da306cf87f033c72ddb745f3077775/',
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
906 'name': 'MinimalistTheme'
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
907 })
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
908 elif plugins['theme'] == 'Dark':
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
909 extra_data['plugins'].append({
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
910 'location': 'https://cdn.rawgit.com/erasche/jbrowse-dark-theme/689eceb7e33bbc1b9b15518d45a5a79b2e5d0a26/',
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
911 'name': 'DarkTheme'
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
912 })
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
913
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
914 GALAXY_INFRASTRUCTURE_URL = root.find('metadata/galaxyUrl').text
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
915 # Sometimes this comes as `localhost` without a protocol
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
916 if not GALAXY_INFRASTRUCTURE_URL.startswith('http'):
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
917 # so we'll prepend `http://` and hope for the best. Requests *should*
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
918 # be GET and not POST so it should redirect OK
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
919 GALAXY_INFRASTRUCTURE_URL = 'http://' + GALAXY_INFRASTRUCTURE_URL
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
920
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
921 for track in root.findall('tracks/track'):
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
922 track_conf = {}
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
923 track_conf['trackfiles'] = []
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
924
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
925 for x in track.findall('files/trackFile'):
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
926 metadata = metadata_from_node(x.find('metadata'))
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
927
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
928 track_conf['trackfiles'].append((
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
929 os.path.realpath(x.attrib['path']),
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
930 x.attrib['ext'],
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
931 x.attrib['label'],
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
932 metadata
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
933 ))
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
934
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
935 track_conf['category'] = track.attrib['cat']
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
936 track_conf['format'] = track.attrib['format']
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iuc
parents: 1
diff changeset
937 try:
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iuc
parents: 1
diff changeset
938 # Only pertains to gff3 + blastxml. TODO?
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
939 track_conf['style'] = {t.tag: t.text for t in track.find('options/style')}
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
940 except TypeError as te:
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
941 track_conf['style'] = {}
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
942 pass
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
943 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
iuc
parents: 3
diff changeset
944 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
945
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
946 for key in keys:
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
947 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
iuc
parents: 3
diff changeset
948
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
949 jc.add_final_data(extra_data)
20
558d652cd681 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 75a0a1c7b26cac156f76e8266a0e2e3d81be7f02
iuc
parents: 17
diff changeset
950 jc.generate_names()