Mercurial > repos > iuc > jbrowse
annotate jbrowse.py @ 3:7342f467507b draft
Uploaded v0.4 of JBrowse
| author | iuc |
|---|---|
| date | Thu, 31 Dec 2015 13:58:43 -0500 |
| parents | 497c6bb3b717 |
| children | ae9382cfb6ac |
| rev | line source |
|---|---|
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0
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff
changeset
|
1 #!/usr/bin/env python |
|
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff
changeset
|
2 import os |
| 3 | 3 import copy |
|
0
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff
changeset
|
4 import argparse |
|
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff
changeset
|
5 import subprocess |
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2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff
changeset
|
6 import hashlib |
| 3 | 7 import struct |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
8 import tempfile |
| 3 | 9 import shutil |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
10 import json |
| 3 | 11 from Bio.Data import CodonTable |
| 12 import xml.etree.ElementTree as ET | |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
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13 import logging |
| 3 | 14 from collections import defaultdict |
| 15 logging.basicConfig(level=logging.INFO) | |
| 16 log = logging.getLogger('jbrowse') | |
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1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
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17 |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
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18 |
| 3 | 19 class ColorScaling(object): |
| 20 | |
| 21 COLOR_FUNCTION_TEMPLATE = """ | |
| 22 function(feature, variableName, glyphObject, track) {{ | |
| 23 var score = {score}; | |
| 24 {opacity} | |
| 25 return 'rgba({red}, {green}, {blue}, ' + opacity + ')'; | |
| 26 }} | |
| 27 """ | |
| 28 | |
| 29 COLOR_FUNCTION_TEMPLATE_QUAL = """ | |
| 30 function(feature, variableName, glyphObject, track) {{ | |
| 31 var search_up = function self(sf, attr){{ | |
| 32 if(sf.get(attr) !== undefined){{ | |
| 33 return sf.get(attr); | |
| 34 }} | |
| 35 if(sf.parent() === undefined) {{ | |
| 36 return; | |
| 37 }}else{{ | |
| 38 return self(sf.parent(), attr); | |
| 39 }} | |
| 40 }}; | |
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0
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff
changeset
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41 |
| 3 | 42 var search_down = function self(sf, attr){{ |
| 43 if(sf.get(attr) !== undefined){{ | |
| 44 return sf.get(attr); | |
| 45 }} | |
| 46 if(sf.children() === undefined) {{ | |
| 47 return; | |
| 48 }}else{{ | |
| 49 var kids = sf.children(); | |
| 50 for(var child_idx in kids){{ | |
| 51 var x = self(kids[child_idx], attr); | |
| 52 if(x !== undefined){{ | |
| 53 return x; | |
| 54 }} | |
| 55 }} | |
| 56 return; | |
| 57 }} | |
| 58 }}; | |
| 59 | |
| 60 var color = ({user_spec_color} || search_up(feature, 'color') || search_down(feature, 'color') || {auto_gen_color}); | |
| 61 var score = (search_up(feature, 'score') || search_down(feature, 'score')); | |
| 62 {opacity} | |
| 63 var result = /^#?([a-f\d]{{2}})([a-f\d]{{2}})([a-f\d]{{2}})$/i.exec(color); | |
| 64 var red = parseInt(result[1], 16); | |
| 65 var green = parseInt(result[2], 16); | |
| 66 var blue = parseInt(result[3], 16); | |
| 67 if(isNaN(opacity) || opacity < 0){{ opacity = 0; }} | |
| 68 return 'rgba(' + red + ',' + green + ',' + blue + ',' + opacity + ')'; | |
| 69 }} | |
| 70 """ | |
|
0
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff
changeset
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71 |
| 3 | 72 OPACITY_MATH = { |
| 73 'linear': """ | |
| 74 var opacity = (score - ({min})) / (({max}) - ({min})); | |
| 75 """, | |
| 76 'logarithmic': """ | |
| 77 var opacity = (score - ({min})) / (({max}) - ({min})); | |
| 78 opacity = Math.log10(opacity) + Math.log10({max}); | |
| 79 """, | |
| 80 'blast': """ | |
| 81 var opacity = 0; | |
| 82 if(score == 0.0) { | |
| 83 opacity = 1; | |
| 84 } else{ | |
| 85 opacity = (20 - Math.log10(score)) / 180; | |
| 86 } | |
| 87 """ | |
| 88 } | |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
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89 |
| 3 | 90 BREWER_COLOUR_IDX = 0 |
| 91 BREWER_COLOUR_SCHEMES = [ | |
| 92 (166, 206, 227), | |
| 93 (31, 120, 180), | |
| 94 (178, 223, 138), | |
| 95 (51, 160, 44), | |
| 96 (251, 154, 153), | |
| 97 (227, 26, 28), | |
| 98 (253, 191, 111), | |
| 99 (255, 127, 0), | |
| 100 (202, 178, 214), | |
| 101 (106, 61, 154), | |
| 102 (255, 255, 153), | |
| 103 (177, 89, 40), | |
| 104 (228, 26, 28), | |
| 105 (55, 126, 184), | |
| 106 (77, 175, 74), | |
| 107 (152, 78, 163), | |
| 108 (255, 127, 0), | |
| 109 ] | |
| 110 | |
| 111 BREWER_DIVERGING_PALLETES = { | |
| 112 'BrBg': ("#543005", "#003c30"), | |
| 113 'PiYg': ("#8e0152", "#276419"), | |
| 114 'PRGn': ("#40004b", "#00441b"), | |
| 115 'PuOr': ("#7f3b08", "#2d004b"), | |
| 116 'RdBu': ("#67001f", "#053061"), | |
| 117 'RdGy': ("#67001f", "#1a1a1a"), | |
| 118 'RdYlBu': ("#a50026", "#313695"), | |
| 119 'RdYlGn': ("#a50026", "#006837"), | |
| 120 'Spectral': ("#9e0142", "#5e4fa2"), | |
| 121 } | |
| 122 | |
| 123 def __init__(self): | |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
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124 self.brewer_colour_idx = 0 |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
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125 |
| 3 | 126 def rgb_from_hex(self, hexstr): |
| 127 # http://stackoverflow.com/questions/4296249/how-do-i-convert-a-hex-triplet-to-an-rgb-tuple-and-back | |
| 128 return struct.unpack('BBB',hexstr.decode('hex')) | |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
129 |
| 3 | 130 def min_max_gff(self, gff_file): |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
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131 min_val = None |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
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132 max_val = None |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
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133 with open(gff_file, 'r') as handle: |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
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134 for line in handle: |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
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135 try: |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
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136 value = float(line.split('\t')[5]) |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
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137 min_val = min(value, (min_val or value)) |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
138 max_val = max(value, (max_val or value)) |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
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139 |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
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140 if value < min_val: |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
141 min_val = value |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
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142 |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
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143 if value > max_val: |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
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144 max_val = value |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
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145 except Exception: |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
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146 pass |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
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147 return min_val, max_val |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
148 |
| 3 | 149 def hex_from_rgb(self, r, g, b): |
| 150 return '#%02x%02x%02x' % (r, g, b) | |
| 151 | |
| 152 def _get_colours(self): | |
| 153 r, g, b = self.BREWER_COLOUR_SCHEMES[self.brewer_colour_idx] | |
| 154 self.brewer_colour_idx += 1 | |
| 155 return r, g, b | |
| 156 | |
| 157 def parse_colours(self, track, trackFormat, gff3=None): | |
| 158 # Wiggle tracks have a bicolor pallete | |
| 159 trackConfig = {'style': {}} | |
| 160 if trackFormat == 'wiggle': | |
| 161 | |
| 162 trackConfig['style']['pos_color'] = track['wiggle']['color_pos'] | |
| 163 trackConfig['style']['neg_color'] = track['wiggle']['color_neg'] | |
| 164 | |
| 165 if trackConfig['style']['pos_color'] == '__auto__': | |
| 166 trackConfig['style']['neg_color'] = self.hex_from_rgb(*self._get_colours()) | |
| 167 trackConfig['style']['pos_color'] = self.hex_from_rgb(*self._get_colours()) | |
| 168 | |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
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169 |
| 3 | 170 # Wiggle tracks can change colour at a specified place |
| 171 bc_pivot = track['wiggle']['bicolor_pivot'] | |
| 172 if bc_pivot not in ('mean', 'zero'): | |
| 173 # The values are either one of those two strings | |
| 174 # or a number | |
| 175 bc_pivot = float(bc_pivot) | |
| 176 trackConfig['bicolor_pivot'] = bc_pivot | |
| 177 elif 'scaling' in track: | |
| 178 if track['scaling']['method'] == 'ignore': | |
| 179 if track['scaling']['scheme']['color'] != '__auto__': | |
| 180 trackConfig['style']['color'] = track['scaling']['scheme']['color'] | |
| 181 else: | |
| 182 trackConfig['style']['color'] = self.hex_from_rgb(*self._get_colours()) | |
| 183 else: | |
| 184 # Scored method | |
| 185 algo = track['scaling']['algo'] | |
| 186 # linear, logarithmic, blast | |
| 187 scales = track['scaling']['scales'] | |
| 188 # type __auto__, manual (min, max) | |
| 189 scheme = track['scaling']['scheme'] | |
| 190 # scheme -> (type (opacity), color) | |
| 191 # ================================== | |
| 192 # GENE CALLS OR BLAST | |
| 193 # ================================== | |
| 194 if trackFormat == 'blast': | |
| 195 red, green, blue = self._get_colours() | |
| 196 color_function = self.COLOR_FUNCTION_TEMPLATE.format(**{ | |
| 197 'score': "feature._parent.get('score')", | |
| 198 'opacity': self.OPACITY_MATH['blast'], | |
| 199 'red': red, | |
| 200 'green': green, | |
| 201 'blue': blue, | |
| 202 }) | |
| 203 trackConfig['style']['color'] = color_function.replace('\n', '') | |
| 204 elif trackFormat == 'gene_calls': | |
| 205 # Default values, based on GFF3 spec | |
| 206 min_val = 0 | |
| 207 max_val = 1000 | |
| 208 # Get min/max and build a scoring function since JBrowse doesn't | |
| 209 if scales['type'] == 'automatic': | |
| 210 min_val, max_val = self.min_max_gff(gff3) | |
| 211 else: | |
| 212 min_val = scales['min'] | |
| 213 max_val = scales['max'] | |
| 214 | |
| 215 if scheme['color'] == '__auto__': | |
| 216 user_color = 'undefined' | |
| 217 auto_color = "'%s'" % self.hex_from_rgb(*self._get_colours()) | |
| 218 elif scheme['color'].startswith('#'): | |
| 219 user_color = "'%s'" % self.hex_from_rgb(*self.rgb_from_hex(scheme['color'][1:])) | |
| 220 auto_color = 'undefined' | |
| 221 else: | |
| 222 user_color = 'undefined' | |
| 223 auto_color = "'%s'" % self.hex_from_rgb(*self._get_colours()) | |
| 224 | |
| 225 color_function = self.COLOR_FUNCTION_TEMPLATE_QUAL.format(**{ | |
| 226 'opacity': self.OPACITY_MATH[algo].format(**{'max': max_val,'min': min_val}), | |
| 227 'user_spec_color': user_color, | |
| 228 'auto_gen_color': auto_color, | |
| 229 }) | |
| 230 | |
| 231 trackConfig['style']['color'] = color_function.replace('\n', '') | |
| 232 return trackConfig | |
| 233 | |
| 234 | |
| 235 def etree_to_dict(t): | |
| 236 d = {t.tag: {} if t.attrib else None} | |
| 237 children = list(t) | |
| 238 if children: | |
| 239 dd = defaultdict(list) | |
| 240 for dc in map(etree_to_dict, children): | |
| 241 for k, v in dc.iteritems(): | |
| 242 dd[k].append(v) | |
| 243 d = {t.tag: {k:v[0] if len(v) == 1 else v for k, v in dd.iteritems()}} | |
| 244 if t.attrib: | |
| 245 d[t.tag].update(('@' + k, v) for k, v in t.attrib.iteritems()) | |
| 246 if t.text: | |
| 247 text = t.text.strip() | |
| 248 if children or t.attrib: | |
| 249 if text: | |
| 250 d[t.tag]['#text'] = text | |
| 251 else: | |
| 252 d[t.tag] = text | |
| 253 return d | |
| 254 | |
| 255 | |
| 256 # score comes from feature._parent.get('score') or feature.get('score') | |
| 257 | |
| 258 INSTALLED_TO = os.path.dirname(os.path.realpath(__file__)) | |
| 259 | |
| 260 | |
| 261 class JbrowseConnector(object): | |
| 262 | |
| 263 def __init__(self, jbrowse, outdir, genomes, standalone=False, gencode=1): | |
| 264 self.TN_TABLE = { | |
| 265 'gff3': '--gff', | |
| 266 'gff': '--gff', | |
| 267 'bed': '--bed', | |
| 268 'genbank': '--gbk', | |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
269 } |
| 3 | 270 |
| 271 self.cs = ColorScaling() | |
| 272 self.jbrowse = jbrowse | |
| 273 self.outdir = outdir | |
| 274 self.genome_paths = genomes | |
| 275 self.standalone = standalone | |
| 276 self.gencode = gencode | |
| 277 | |
| 278 if standalone: | |
| 279 self.clone_jbrowse(self.jbrowse, self.outdir) | |
| 280 else: | |
| 281 try: | |
| 282 os.makedirs(self.outdir) | |
| 283 except OSError: | |
| 284 # Ignore if the folder exists | |
| 285 pass | |
| 286 | |
| 287 self.process_genomes() | |
| 288 self.update_gencode() | |
| 289 | |
| 290 def update_gencode(self): | |
| 291 table = CodonTable.unambiguous_dna_by_id[int(self.gencode)] | |
| 292 trackList = os.path.join(self.outdir, 'data', 'trackList.json') | |
| 293 with open(trackList, 'r') as handle: | |
| 294 trackListData = json.load(handle) | |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
295 |
| 3 | 296 trackListData['tracks'][0].update({ |
| 297 'codonStarts': table.start_codons, | |
| 298 'codonStops': table.stop_codons, | |
| 299 'codonTable': table.forward_table, | |
| 300 }) | |
| 301 | |
| 302 with open(trackList, 'w') as handle: | |
| 303 json.dump(trackListData, handle, indent=2) | |
| 304 | |
| 305 | |
| 306 def subprocess_check_call(self, command): | |
| 307 log.debug('cd %s && %s', self.outdir, ' '.join(command)) | |
| 308 subprocess.check_call(command, cwd=self.outdir) | |
| 309 | |
| 310 def _jbrowse_bin(self, command): | |
| 311 return os.path.realpath(os.path.join(self.jbrowse, 'bin', command)) | |
| 312 | |
| 313 def process_genomes(self): | |
| 314 for genome_path in self.genome_paths: | |
| 315 self.subprocess_check_call([ | |
| 316 'perl', self._jbrowse_bin('prepare-refseqs.pl'), | |
| 317 '--fasta', genome_path]) | |
| 318 | |
| 319 def _add_json(self, json_data): | |
| 320 if len(json_data.keys()) == 0: | |
| 321 return | |
| 322 | |
| 323 tmp = tempfile.NamedTemporaryFile(delete=False) | |
| 324 tmp.write(json.dumps(json_data)) | |
| 325 tmp.close() | |
| 326 cmd = ['perl', self._jbrowse_bin('add-track-json.pl'), tmp.name, | |
| 327 os.path.join('data', 'trackList.json')] | |
| 328 self.subprocess_check_call(cmd) | |
| 329 os.unlink(tmp.name) | |
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330 |
| 3 | 331 def _add_track_json(self, json_data): |
| 332 if len(json_data.keys()) == 0: | |
| 333 return | |
| 334 | |
| 335 tmp = tempfile.NamedTemporaryFile(delete=False) | |
| 336 tmp.write(json.dumps(json_data)) | |
| 337 tmp.close() | |
| 338 cmd = ['perl', self._jbrowse_bin('add-track-json.pl'), tmp.name, | |
| 339 os.path.join('data', 'trackList.json')] | |
| 340 self.subprocess_check_call(cmd) | |
| 341 os.unlink(tmp.name) | |
| 342 | |
| 343 | |
| 344 def _blastxml_to_gff3(self, xml, min_gap=10): | |
| 345 gff3_unrebased = tempfile.NamedTemporaryFile(delete=False) | |
| 346 cmd = ['python', os.path.join(INSTALLED_TO, 'blastxml_to_gapped_gff3.py'), | |
| 347 '--trim', '--trim_end', '--min_gap', str(min_gap), xml] | |
| 348 log.debug('cd %s && %s > %s', self.outdir, ' '.join(cmd), gff3_unrebased.name) | |
| 349 subprocess.check_call(cmd, cwd=self.outdir, stdout=gff3_unrebased) | |
| 350 gff3_unrebased.close() | |
| 351 return gff3_unrebased.name | |
| 352 | |
| 353 def add_blastxml(self, data, trackData, blastOpts, **kwargs): | |
| 354 gff3 = self._blastxml_to_gff3(data, min_gap=blastOpts['min_gap']) | |
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355 |
| 3 | 356 if 'parent' in blastOpts: |
| 357 gff3_rebased = tempfile.NamedTemporaryFile(delete=False) | |
| 358 cmd = ['python', os.path.join(INSTALLED_TO, 'gff3_rebase.py')] | |
| 359 if blastOpts.get('protein', 'false') == 'true': | |
| 360 cmd.append('--protein2dna') | |
| 361 cmd.extend([os.path.realpath(blastOpts['parent']), gff3]) | |
| 362 log.debug('cd %s && %s > %s', self.outdir, ' '.join(cmd), gff3_rebased.name) | |
| 363 subprocess.check_call(cmd, cwd=self.outdir, stdout=gff3_rebased) | |
| 364 gff3_rebased.close() | |
| 365 | |
| 366 # Replace original gff3 file | |
| 367 shutil.copy(gff3_rebased.name, gff3) | |
| 368 os.unlink(gff3_rebased.name) | |
| 369 | |
| 370 config = { | |
| 371 'glyph': 'JBrowse/View/FeatureGlyph/Segments', | |
| 372 "category": trackData['category'], | |
| 373 } | |
| 374 | |
| 375 clientConfig = trackData['style'] | |
| 376 | |
| 377 cmd = ['perl', self._jbrowse_bin('flatfile-to-json.pl'), | |
| 378 '--gff', gff3, | |
| 379 '--trackLabel', trackData['label'], | |
| 380 '--key', trackData['key'], | |
| 381 '--clientConfig', json.dumps(clientConfig), | |
| 382 '--config', json.dumps(config), | |
| 383 '--trackType', 'JBrowse/View/Track/CanvasFeatures' | |
| 384 ] | |
| 385 | |
| 386 self.subprocess_check_call(cmd) | |
| 387 os.unlink(gff3) | |
| 388 | |
| 389 def add_bigwig(self, data, trackData, wiggleOpts, **kwargs): | |
| 390 dest = os.path.join('data', 'raw', trackData['label'] + '.bw') | |
| 391 cmd = ['ln', data, dest] | |
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392 self.subprocess_check_call(cmd) |
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393 |
| 3 | 394 trackData.update({ |
| 395 "urlTemplate": os.path.join('..', dest), | |
| 396 "storeClass": "JBrowse/Store/SeqFeature/BigWig", | |
| 397 "type": "JBrowse/View/Track/Wiggle/Density", | |
| 398 }) | |
| 399 | |
| 400 trackData['type'] = wiggleOpts['type'] | |
| 401 trackData['variance_band'] = True if wiggleOpts['variance_band'] == 'true' else False | |
| 402 | |
| 403 if 'min' in wiggleOpts and 'max' in wiggleOpts: | |
| 404 trackData['min_score'] = wiggleOpts['min'] | |
| 405 trackData['max_score'] = wiggleOpts['max'] | |
| 406 else: | |
| 407 trackData['autoscale'] = wiggleOpts.get('autoscale', 'local') | |
| 408 | |
| 409 self._add_track_json(trackData) | |
| 410 | |
| 411 def add_bam(self, data, trackData, bamOpts, bam_index=None, **kwargs): | |
| 412 dest = os.path.join('data', 'raw', trackData['label'] + '.bam') | |
| 413 cmd = ['ln', '-s', os.path.realpath(data), dest] | |
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414 self.subprocess_check_call(cmd) |
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415 |
| 3 | 416 cmd = ['ln', '-s', os.path.realpath(bam_index), dest + '.bai'] |
| 417 self.subprocess_check_call(cmd) | |
| 418 | |
| 419 trackData.update({ | |
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420 "urlTemplate": os.path.join('..', dest), |
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421 "type": "JBrowse/View/Track/Alignments2", |
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422 "storeClass": "JBrowse/Store/SeqFeature/BAM", |
| 3 | 423 }) |
| 424 | |
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425 |
| 3 | 426 self._add_track_json(trackData) |
| 427 | |
| 428 if bamOpts.get('auto_snp', 'false') == 'true': | |
| 429 trackData2 = copy.copy(trackData) | |
| 430 trackData2.update({ | |
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431 "type": "JBrowse/View/Track/SNPCoverage", |
| 3 | 432 "key": trackData['key'] + " - SNPs/Coverage", |
| 433 "label": trackData['label'] + "_autosnp", | |
| 434 }) | |
| 435 self._add_track_json(trackData2) | |
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436 |
| 3 | 437 def add_vcf(self, data, trackData, vcfOpts={}, **kwargs): |
| 438 dest = os.path.join('data', 'raw', trackData['label'] + '.vcf') | |
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439 # ln? |
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440 cmd = ['ln', '-s', data, dest] |
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441 self.subprocess_check_call(cmd) |
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442 cmd = ['bgzip', dest] |
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443 self.subprocess_check_call(cmd) |
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444 cmd = ['tabix', '-p', 'vcf', dest + '.gz'] |
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445 self.subprocess_check_call(cmd) |
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446 |
| 3 | 447 trackData.update({ |
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448 "urlTemplate": os.path.join('..', dest + '.gz'), |
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449 "type": "JBrowse/View/Track/HTMLVariants", |
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450 "storeClass": "JBrowse/Store/SeqFeature/VCFTabix", |
| 3 | 451 }) |
| 452 self._add_track_json(trackData) | |
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453 |
| 3 | 454 def add_features(self, data, format, trackData, gffOpts, **kwargs): |
| 455 cmd = [ | |
| 456 'perl', self._jbrowse_bin('flatfile-to-json.pl'), | |
| 457 self.TN_TABLE.get(format, 'gff'), | |
| 458 data, | |
| 459 '--trackLabel', trackData['label'], | |
| 460 '--trackType', 'JBrowse/View/Track/CanvasFeatures', | |
| 461 '--key', trackData['key'] | |
| 462 ] | |
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463 |
| 3 | 464 config = copy.copy(trackData) |
| 465 clientConfig = trackData['style'] | |
| 466 del config['style'] | |
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467 |
| 3 | 468 if 'match' in gffOpts: |
|
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469 config['glyph'] = 'JBrowse/View/FeatureGlyph/Segments' |
| 3 | 470 cmd += ['--type', gffOpts['match']] |
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471 |
| 3 | 472 cmd += ['--clientConfig', json.dumps(clientConfig), |
| 473 '--trackType', 'JBrowse/View/Track/CanvasFeatures' | |
| 474 ] | |
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475 |
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476 cmd.extend(['--config', json.dumps(config)]) |
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477 |
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478 self.subprocess_check_call(cmd) |
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479 |
| 3 | 480 |
| 481 def process_annotations(self, track): | |
| 482 outputTrackConfig = { | |
| 483 'style': { | |
| 484 'label': track['style'].get('label', 'description'), | |
| 485 'className': track['style'].get('className', 'feature'), | |
| 486 'description': track['style'].get('description', ''), | |
| 487 }, | |
| 488 'category': track['category'], | |
| 489 } | |
| 490 | |
| 491 for i, (dataset_path, dataset_ext, track_human_label) in enumerate(track['trackfiles']): | |
| 492 log.info('Processing %s / %s', track['category'], track_human_label) | |
| 493 outputTrackConfig['key'] = track_human_label | |
| 494 hashData = [dataset_path, track_human_label, track['category']] | |
| 495 outputTrackConfig['label'] = hashlib.md5('|'.join(hashData)).hexdigest() + '_%s' % i | |
| 496 | |
| 497 # Colour parsing is complex due to different track types having | |
| 498 # different colour options. | |
| 499 colourOptions = self.cs.parse_colours(track['conf']['options'], track['format'], gff3=dataset_path) | |
| 500 # This used to be done with a dict.update() call, however that wiped out any previous style settings... | |
| 501 for key in colourOptions: | |
| 502 if key == 'style': | |
| 503 for subkey in colourOptions['style']: | |
| 504 outputTrackConfig['style'][subkey] = colourOptions['style'][subkey] | |
| 505 else: | |
| 506 outputTrackConfig[key] = colourOptions[key] | |
| 507 | |
| 508 if dataset_ext in ('gff', 'gff3', 'bed'): | |
| 509 self.add_features(dataset_path, dataset_ext, outputTrackConfig, | |
| 510 track['conf']['options']['gff']) | |
| 511 elif dataset_ext == 'bigwig': | |
| 512 self.add_bigwig(dataset_path, outputTrackConfig, | |
| 513 track['conf']['options']['wiggle']) | |
| 514 elif dataset_ext == 'bam': | |
| 515 real_indexes = track['conf']['options']['pileup']['bam_indices']['bam_index'] | |
| 516 if not isinstance(real_indexes, list): | |
| 517 # <bam_indices> | |
| 518 # <bam_index>/path/to/a.bam.bai</bam_index> | |
| 519 # </bam_indices> | |
| 520 # | |
| 521 # The above will result in the 'bam_index' key containing a | |
| 522 # string. If there are two or more indices, the container | |
| 523 # becomes a list. Fun! | |
| 524 real_indexes = [real_indexes] | |
| 525 | |
| 526 self.add_bam(dataset_path, outputTrackConfig, | |
| 527 track['conf']['options']['pileup'], | |
| 528 bam_index=real_indexes[i]) | |
| 529 elif dataset_ext == 'blastxml': | |
| 530 self.add_blastxml(dataset_path, outputTrackConfig, track['conf']['options']['blast']) | |
| 531 elif dataset_ext == 'vcf': | |
| 532 self.add_vcf(dataset_path, outputTrackConfig) | |
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533 |
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534 def clone_jbrowse(self, jbrowse_dir, destination): |
| 3 | 535 """Clone a JBrowse directory into a destination directory. |
| 536 """ | |
|
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537 # JBrowse seems to have included some bad symlinks, cp ignores bad symlinks |
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538 # unlike copytree |
| 3 | 539 cmd = ['cp', '-r', os.path.join(jbrowse_dir, '.'), destination] |
| 540 log.debug(' '.join(cmd)) | |
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541 subprocess.check_call(cmd) |
| 3 | 542 cmd = ['mkdir', '-p', os.path.join(destination, 'data', 'raw')] |
| 543 log.debug(' '.join(cmd)) | |
|
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544 subprocess.check_call(cmd) |
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545 |
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546 # http://unix.stackexchange.com/a/38691/22785 |
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547 # JBrowse releases come with some broken symlinks |
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548 cmd = ['find', destination, '-type', 'l', '-xtype', 'l', '-exec', 'rm', "'{}'", '+'] |
| 3 | 549 log.debug(' '.join(cmd)) |
|
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550 subprocess.check_call(cmd) |
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551 |
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552 |
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553 if __name__ == '__main__': |
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554 parser = argparse.ArgumentParser(description="", epilog="") |
| 3 | 555 parser.add_argument('xml', type=file, help='Track Configuration') |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
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556 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
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557 parser.add_argument('--jbrowse', help='Folder containing a jbrowse release') |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
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558 parser.add_argument('--outdir', help='Output directory', default='out') |
| 3 | 559 parser.add_argument('--standalone', help='Standalone mode includes a copy of JBrowse', action='store_true') |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
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560 args = parser.parse_args() |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
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561 |
| 3 | 562 tree = ET.parse(args.xml.name) |
| 563 root = tree.getroot() | |
| 564 | |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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565 jc = JbrowseConnector( |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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566 jbrowse=args.jbrowse, |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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567 outdir=args.outdir, |
| 3 | 568 genomes=[os.path.realpath(x.text) for x in root.findall('metadata/genomes/genome')], |
| 569 standalone=args.standalone, | |
| 570 gencode=root.find('metadata/gencode').text | |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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571 ) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
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572 |
| 3 | 573 for track in root.findall('tracks/track'): |
| 574 track_conf = {} | |
| 575 track_conf['trackfiles'] = [ | |
| 576 (os.path.realpath(x.attrib['path']), x.attrib['ext'], x.attrib['label']) | |
| 577 for x in track.findall('files/trackFile') | |
| 578 ] | |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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579 |
| 3 | 580 track_conf['category'] = track.attrib['cat'] |
| 581 track_conf['format'] = track.attrib['format'] | |
| 582 try: | |
| 583 # Only pertains to gff3 + blastxml. TODO? | |
| 584 track_conf['style'] = {t.tag: t.text for t in track.find('options/style')} | |
| 585 except TypeError, te: | |
| 586 track_conf['style'] = {} | |
| 587 pass | |
| 588 track_conf['conf'] = etree_to_dict(track.find('options')) | |
| 589 jc.process_annotations(track_conf) |