Mercurial > repos > iuc > jbrowse
annotate jbrowse.py @ 10:1a6d882d340d draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
| author | iuc |
|---|---|
| date | Fri, 02 Dec 2016 17:58:54 -0500 |
| parents | ad4b9d7eae6a |
| children | 4cbceec1d6b4 |
| rev | line source |
|---|---|
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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
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1 #!/usr/bin/env python |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
5
diff
changeset
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2 import argparse |
| 3 | 3 import copy |
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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
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4 import hashlib |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
5
diff
changeset
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5 import json |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
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diff
changeset
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6 import logging |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
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diff
changeset
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7 import os |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
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diff
changeset
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8 import shutil |
| 3 | 9 import struct |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
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diff
changeset
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10 import subprocess |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
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changeset
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11 import tempfile |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
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diff
changeset
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12 import xml.etree.ElementTree as ET |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
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changeset
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13 from collections import defaultdict |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
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14 |
| 3 | 15 from Bio.Data import CodonTable |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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changeset
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16 |
| 3 | 17 logging.basicConfig(level=logging.INFO) |
| 18 log = logging.getLogger('jbrowse') | |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
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changeset
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19 |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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20 |
| 3 | 21 class ColorScaling(object): |
| 22 | |
| 23 COLOR_FUNCTION_TEMPLATE = """ | |
| 24 function(feature, variableName, glyphObject, track) {{ | |
| 25 var score = {score}; | |
| 26 {opacity} | |
| 27 return 'rgba({red}, {green}, {blue}, ' + opacity + ')'; | |
| 28 }} | |
| 29 """ | |
| 30 | |
| 31 COLOR_FUNCTION_TEMPLATE_QUAL = """ | |
| 32 function(feature, variableName, glyphObject, track) {{ | |
| 33 var search_up = function self(sf, attr){{ | |
| 34 if(sf.get(attr) !== undefined){{ | |
| 35 return sf.get(attr); | |
| 36 }} | |
| 37 if(sf.parent() === undefined) {{ | |
| 38 return; | |
| 39 }}else{{ | |
| 40 return self(sf.parent(), attr); | |
| 41 }} | |
| 42 }}; | |
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2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
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changeset
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43 |
| 3 | 44 var search_down = function self(sf, attr){{ |
| 45 if(sf.get(attr) !== undefined){{ | |
| 46 return sf.get(attr); | |
| 47 }} | |
| 48 if(sf.children() === undefined) {{ | |
| 49 return; | |
| 50 }}else{{ | |
| 51 var kids = sf.children(); | |
| 52 for(var child_idx in kids){{ | |
| 53 var x = self(kids[child_idx], attr); | |
| 54 if(x !== undefined){{ | |
| 55 return x; | |
| 56 }} | |
| 57 }} | |
| 58 return; | |
| 59 }} | |
| 60 }}; | |
| 61 | |
| 62 var color = ({user_spec_color} || search_up(feature, 'color') || search_down(feature, 'color') || {auto_gen_color}); | |
| 63 var score = (search_up(feature, 'score') || search_down(feature, 'score')); | |
| 64 {opacity} | |
| 65 var result = /^#?([a-f\d]{{2}})([a-f\d]{{2}})([a-f\d]{{2}})$/i.exec(color); | |
| 66 var red = parseInt(result[1], 16); | |
| 67 var green = parseInt(result[2], 16); | |
| 68 var blue = parseInt(result[3], 16); | |
| 69 if(isNaN(opacity) || opacity < 0){{ opacity = 0; }} | |
| 70 return 'rgba(' + red + ',' + green + ',' + blue + ',' + opacity + ')'; | |
| 71 }} | |
| 72 """ | |
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2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
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73 |
| 3 | 74 OPACITY_MATH = { |
| 75 'linear': """ | |
| 76 var opacity = (score - ({min})) / (({max}) - ({min})); | |
| 77 """, | |
| 78 'logarithmic': """ | |
| 79 var opacity = (score - ({min})) / (({max}) - ({min})); | |
| 80 opacity = Math.log10(opacity) + Math.log10({max}); | |
| 81 """, | |
| 82 'blast': """ | |
| 83 var opacity = 0; | |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
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diff
changeset
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84 if(score == 0.0) { |
| 3 | 85 opacity = 1; |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
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diff
changeset
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86 } else{ |
| 3 | 87 opacity = (20 - Math.log10(score)) / 180; |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
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changeset
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88 } |
| 3 | 89 """ |
| 90 } | |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
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changeset
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91 |
| 3 | 92 BREWER_COLOUR_IDX = 0 |
| 93 BREWER_COLOUR_SCHEMES = [ | |
| 94 (166, 206, 227), | |
| 95 (31, 120, 180), | |
| 96 (178, 223, 138), | |
| 97 (51, 160, 44), | |
| 98 (251, 154, 153), | |
| 99 (227, 26, 28), | |
| 100 (253, 191, 111), | |
| 101 (255, 127, 0), | |
| 102 (202, 178, 214), | |
| 103 (106, 61, 154), | |
| 104 (255, 255, 153), | |
| 105 (177, 89, 40), | |
| 106 (228, 26, 28), | |
| 107 (55, 126, 184), | |
| 108 (77, 175, 74), | |
| 109 (152, 78, 163), | |
| 110 (255, 127, 0), | |
| 111 ] | |
| 112 | |
| 113 BREWER_DIVERGING_PALLETES = { | |
| 114 'BrBg': ("#543005", "#003c30"), | |
| 115 'PiYg': ("#8e0152", "#276419"), | |
| 116 'PRGn': ("#40004b", "#00441b"), | |
| 117 'PuOr': ("#7f3b08", "#2d004b"), | |
| 118 'RdBu': ("#67001f", "#053061"), | |
| 119 'RdGy': ("#67001f", "#1a1a1a"), | |
| 120 'RdYlBu': ("#a50026", "#313695"), | |
| 121 'RdYlGn': ("#a50026", "#006837"), | |
| 122 'Spectral': ("#9e0142", "#5e4fa2"), | |
| 123 } | |
| 124 | |
| 125 def __init__(self): | |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
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changeset
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126 self.brewer_colour_idx = 0 |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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127 |
| 3 | 128 def rgb_from_hex(self, hexstr): |
| 129 # http://stackoverflow.com/questions/4296249/how-do-i-convert-a-hex-triplet-to-an-rgb-tuple-and-back | |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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130 return struct.unpack('BBB', hexstr.decode('hex')) |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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131 |
| 3 | 132 def min_max_gff(self, gff_file): |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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133 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:
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diff
changeset
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134 max_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:
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135 with open(gff_file, 'r') as handle: |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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136 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
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137 try: |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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138 value = float(line.split('\t')[5]) |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
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139 min_val = min(value, (min_val or value)) |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
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140 max_val = max(value, (max_val or value)) |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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141 |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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142 if value < min_val: |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
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143 min_val = value |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
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144 |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
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145 if value > max_val: |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
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146 max_val = value |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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147 except Exception: |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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148 pass |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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149 return min_val, max_val |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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150 |
| 3 | 151 def hex_from_rgb(self, r, g, b): |
| 152 return '#%02x%02x%02x' % (r, g, b) | |
| 153 | |
| 154 def _get_colours(self): | |
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ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
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155 r, g, b = self.BREWER_COLOUR_SCHEMES[self.brewer_colour_idx % len(self.BREWER_COLOUR_SCHEMES)] |
| 3 | 156 self.brewer_colour_idx += 1 |
| 157 return r, g, b | |
| 158 | |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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159 def parse_menus(self, track): |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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160 trackConfig = {'menuTemplate': [{}, {}, {}]} |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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161 |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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162 if 'menu' in track['menus']: |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
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163 menu_list = [track['menus']['menu']] |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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164 if isinstance(track['menus']['menu'], list): |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
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165 menu_list = track['menus']['menu'] |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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166 |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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167 for m in menu_list: |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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168 tpl = { |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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169 'action': m['action'], |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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170 'label': m.get('label', '{name}'), |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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171 'iconClass': m.get('iconClass', 'dijitIconBookmark'), |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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172 } |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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173 if 'url' in m: |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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174 tpl['url'] = m['url'] |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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175 if 'content' in m: |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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176 tpl['content'] = m['content'] |
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177 if 'title' in m: |
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178 tpl['title'] = m['title'] |
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179 |
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180 trackConfig['menuTemplate'].append(tpl) |
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181 |
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182 return trackConfig |
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183 |
| 3 | 184 def parse_colours(self, track, trackFormat, gff3=None): |
| 185 # Wiggle tracks have a bicolor pallete | |
| 186 trackConfig = {'style': {}} | |
| 187 if trackFormat == 'wiggle': | |
| 188 | |
| 189 trackConfig['style']['pos_color'] = track['wiggle']['color_pos'] | |
| 190 trackConfig['style']['neg_color'] = track['wiggle']['color_neg'] | |
| 191 | |
| 192 if trackConfig['style']['pos_color'] == '__auto__': | |
| 193 trackConfig['style']['neg_color'] = self.hex_from_rgb(*self._get_colours()) | |
| 194 trackConfig['style']['pos_color'] = self.hex_from_rgb(*self._get_colours()) | |
| 195 | |
| 196 # Wiggle tracks can change colour at a specified place | |
| 197 bc_pivot = track['wiggle']['bicolor_pivot'] | |
| 198 if bc_pivot not in ('mean', 'zero'): | |
| 199 # The values are either one of those two strings | |
| 200 # or a number | |
| 201 bc_pivot = float(bc_pivot) | |
| 202 trackConfig['bicolor_pivot'] = bc_pivot | |
| 203 elif 'scaling' in track: | |
| 204 if track['scaling']['method'] == 'ignore': | |
| 205 if track['scaling']['scheme']['color'] != '__auto__': | |
| 206 trackConfig['style']['color'] = track['scaling']['scheme']['color'] | |
| 207 else: | |
| 208 trackConfig['style']['color'] = self.hex_from_rgb(*self._get_colours()) | |
| 209 else: | |
| 210 # Scored method | |
| 211 algo = track['scaling']['algo'] | |
| 212 # linear, logarithmic, blast | |
| 213 scales = track['scaling']['scales'] | |
| 214 # type __auto__, manual (min, max) | |
| 215 scheme = track['scaling']['scheme'] | |
| 216 # scheme -> (type (opacity), color) | |
| 217 # ================================== | |
| 218 # GENE CALLS OR BLAST | |
| 219 # ================================== | |
| 220 if trackFormat == 'blast': | |
| 221 red, green, blue = self._get_colours() | |
| 222 color_function = self.COLOR_FUNCTION_TEMPLATE.format(**{ | |
| 223 'score': "feature._parent.get('score')", | |
| 224 'opacity': self.OPACITY_MATH['blast'], | |
| 225 'red': red, | |
| 226 'green': green, | |
| 227 'blue': blue, | |
| 228 }) | |
| 229 trackConfig['style']['color'] = color_function.replace('\n', '') | |
| 230 elif trackFormat == 'gene_calls': | |
| 231 # Default values, based on GFF3 spec | |
| 232 min_val = 0 | |
| 233 max_val = 1000 | |
| 234 # Get min/max and build a scoring function since JBrowse doesn't | |
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235 if scales['type'] == 'automatic' or scales['type'] == '__auto__': |
| 3 | 236 min_val, max_val = self.min_max_gff(gff3) |
| 237 else: | |
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238 min_val = scales.get('min', 0) |
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239 max_val = scales.get('max', 1000) |
| 3 | 240 |
| 241 if scheme['color'] == '__auto__': | |
| 242 user_color = 'undefined' | |
| 243 auto_color = "'%s'" % self.hex_from_rgb(*self._get_colours()) | |
| 244 elif scheme['color'].startswith('#'): | |
| 245 user_color = "'%s'" % self.hex_from_rgb(*self.rgb_from_hex(scheme['color'][1:])) | |
| 246 auto_color = 'undefined' | |
| 247 else: | |
| 248 user_color = 'undefined' | |
| 249 auto_color = "'%s'" % self.hex_from_rgb(*self._get_colours()) | |
| 250 | |
| 251 color_function = self.COLOR_FUNCTION_TEMPLATE_QUAL.format(**{ | |
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252 'opacity': self.OPACITY_MATH[algo].format(**{'max': max_val, 'min': min_val}), |
| 3 | 253 'user_spec_color': user_color, |
| 254 'auto_gen_color': auto_color, | |
| 255 }) | |
| 256 | |
| 257 trackConfig['style']['color'] = color_function.replace('\n', '') | |
| 258 return trackConfig | |
| 259 | |
| 260 | |
| 261 def etree_to_dict(t): | |
| 262 d = {t.tag: {} if t.attrib else None} | |
| 263 children = list(t) | |
| 264 if children: | |
| 265 dd = defaultdict(list) | |
| 266 for dc in map(etree_to_dict, children): | |
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267 for k, v in dc.items(): |
| 3 | 268 dd[k].append(v) |
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269 d = {t.tag: {k: v[0] if len(v) == 1 else v for k, v in dd.items()}} |
| 3 | 270 if t.attrib: |
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271 d[t.tag].update(('@' + k, v) for k, v in t.attrib.items()) |
| 3 | 272 if t.text: |
| 273 text = t.text.strip() | |
| 274 if children or t.attrib: | |
| 275 if text: | |
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276 d[t.tag]['#text'] = text |
| 3 | 277 else: |
| 278 d[t.tag] = text | |
| 279 return d | |
| 280 | |
| 281 | |
| 282 # score comes from feature._parent.get('score') or feature.get('score') | |
| 283 | |
| 284 INSTALLED_TO = os.path.dirname(os.path.realpath(__file__)) | |
| 285 | |
| 286 | |
| 287 class JbrowseConnector(object): | |
| 288 | |
| 289 def __init__(self, jbrowse, outdir, genomes, standalone=False, gencode=1): | |
| 290 self.TN_TABLE = { | |
| 291 'gff3': '--gff', | |
| 292 'gff': '--gff', | |
| 293 'bed': '--bed', | |
| 294 'genbank': '--gbk', | |
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295 } |
| 3 | 296 |
| 297 self.cs = ColorScaling() | |
| 298 self.jbrowse = jbrowse | |
| 299 self.outdir = outdir | |
| 300 self.genome_paths = genomes | |
| 301 self.standalone = standalone | |
| 302 self.gencode = gencode | |
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303 self.tracksToIndex = [] |
| 3 | 304 |
| 305 if standalone: | |
| 306 self.clone_jbrowse(self.jbrowse, self.outdir) | |
| 307 else: | |
| 308 try: | |
| 309 os.makedirs(self.outdir) | |
| 310 except OSError: | |
| 311 # Ignore if the folder exists | |
| 312 pass | |
| 313 | |
| 314 self.process_genomes() | |
| 315 self.update_gencode() | |
| 316 | |
| 317 def update_gencode(self): | |
| 318 table = CodonTable.unambiguous_dna_by_id[int(self.gencode)] | |
| 319 trackList = os.path.join(self.outdir, 'data', 'trackList.json') | |
| 320 with open(trackList, 'r') as handle: | |
| 321 trackListData = json.load(handle) | |
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322 |
| 3 | 323 trackListData['tracks'][0].update({ |
| 324 'codonStarts': table.start_codons, | |
| 325 'codonStops': table.stop_codons, | |
| 326 'codonTable': table.forward_table, | |
| 327 }) | |
| 328 | |
| 329 with open(trackList, 'w') as handle: | |
| 330 json.dump(trackListData, handle, indent=2) | |
| 331 | |
| 332 def subprocess_check_call(self, command): | |
| 333 log.debug('cd %s && %s', self.outdir, ' '.join(command)) | |
| 334 subprocess.check_call(command, cwd=self.outdir) | |
| 335 | |
| 336 def _jbrowse_bin(self, command): | |
| 337 return os.path.realpath(os.path.join(self.jbrowse, 'bin', command)) | |
| 338 | |
| 339 def process_genomes(self): | |
| 340 for genome_path in self.genome_paths: | |
| 341 self.subprocess_check_call([ | |
| 342 'perl', self._jbrowse_bin('prepare-refseqs.pl'), | |
| 343 '--fasta', genome_path]) | |
| 344 | |
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345 def generate_names(self): |
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346 # Generate names |
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347 |
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348 args = [ |
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349 'perl', self._jbrowse_bin('generate-names.pl'), |
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350 '--hashBits', '16' |
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351 ] |
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352 |
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353 tracks = ','.join(self.tracksToIndex) |
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354 |
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355 if tracks: |
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356 args += ['--tracks', tracks] |
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357 else: |
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358 # No tracks to index, index only the refseq |
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359 args += ['--tracks', 'DNA'] |
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360 |
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361 self.subprocess_check_call(args) |
| 3 | 362 |
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363 def _add_json(self, json_data): |
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364 |
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365 cmd = [ |
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366 'perl', self._jbrowse_bin('add-json.pl'), |
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367 json.dumps(json_data), |
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368 os.path.join('data', 'trackList.json') |
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369 ] |
| 3 | 370 self.subprocess_check_call(cmd) |
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371 |
| 3 | 372 def _add_track_json(self, json_data): |
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373 if len(json_data) == 0: |
| 3 | 374 return |
| 375 | |
| 376 tmp = tempfile.NamedTemporaryFile(delete=False) | |
| 377 tmp.write(json.dumps(json_data)) | |
| 378 tmp.close() | |
| 379 cmd = ['perl', self._jbrowse_bin('add-track-json.pl'), tmp.name, | |
| 380 os.path.join('data', 'trackList.json')] | |
| 381 self.subprocess_check_call(cmd) | |
| 382 os.unlink(tmp.name) | |
| 383 | |
| 384 def _blastxml_to_gff3(self, xml, min_gap=10): | |
| 385 gff3_unrebased = tempfile.NamedTemporaryFile(delete=False) | |
| 386 cmd = ['python', os.path.join(INSTALLED_TO, 'blastxml_to_gapped_gff3.py'), | |
| 387 '--trim', '--trim_end', '--min_gap', str(min_gap), xml] | |
| 388 log.debug('cd %s && %s > %s', self.outdir, ' '.join(cmd), gff3_unrebased.name) | |
| 389 subprocess.check_call(cmd, cwd=self.outdir, stdout=gff3_unrebased) | |
| 390 gff3_unrebased.close() | |
| 391 return gff3_unrebased.name | |
| 392 | |
| 393 def add_blastxml(self, data, trackData, blastOpts, **kwargs): | |
| 394 gff3 = self._blastxml_to_gff3(data, min_gap=blastOpts['min_gap']) | |
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395 |
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396 if 'parent' in blastOpts and blastOpts['parent'] != 'None': |
| 3 | 397 gff3_rebased = tempfile.NamedTemporaryFile(delete=False) |
| 398 cmd = ['python', os.path.join(INSTALLED_TO, 'gff3_rebase.py')] | |
| 399 if blastOpts.get('protein', 'false') == 'true': | |
| 400 cmd.append('--protein2dna') | |
| 401 cmd.extend([os.path.realpath(blastOpts['parent']), gff3]) | |
| 402 log.debug('cd %s && %s > %s', self.outdir, ' '.join(cmd), gff3_rebased.name) | |
| 403 subprocess.check_call(cmd, cwd=self.outdir, stdout=gff3_rebased) | |
| 404 gff3_rebased.close() | |
| 405 | |
| 406 # Replace original gff3 file | |
| 407 shutil.copy(gff3_rebased.name, gff3) | |
| 408 os.unlink(gff3_rebased.name) | |
| 409 | |
| 410 config = { | |
| 411 'glyph': 'JBrowse/View/FeatureGlyph/Segments', | |
| 412 "category": trackData['category'], | |
| 413 } | |
| 414 | |
| 415 clientConfig = trackData['style'] | |
| 416 | |
| 417 cmd = ['perl', self._jbrowse_bin('flatfile-to-json.pl'), | |
| 418 '--gff', gff3, | |
| 419 '--trackLabel', trackData['label'], | |
| 420 '--key', trackData['key'], | |
| 421 '--clientConfig', json.dumps(clientConfig), | |
| 422 '--config', json.dumps(config), | |
| 423 '--trackType', 'JBrowse/View/Track/CanvasFeatures' | |
| 424 ] | |
| 425 | |
| 426 self.subprocess_check_call(cmd) | |
| 427 os.unlink(gff3) | |
| 428 | |
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429 if blastOpts.get('index', 'false') == 'true': |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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430 self.tracksToIndex.append("%s" % trackData['label']) |
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431 |
| 3 | 432 def add_bigwig(self, data, trackData, wiggleOpts, **kwargs): |
| 433 dest = os.path.join('data', 'raw', trackData['label'] + '.bw') | |
| 434 cmd = ['ln', data, dest] | |
|
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435 self.subprocess_check_call(cmd) |
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436 |
| 3 | 437 trackData.update({ |
| 438 "urlTemplate": os.path.join('..', dest), | |
| 439 "storeClass": "JBrowse/Store/SeqFeature/BigWig", | |
| 440 "type": "JBrowse/View/Track/Wiggle/Density", | |
| 441 }) | |
| 442 | |
| 443 trackData['type'] = wiggleOpts['type'] | |
| 444 trackData['variance_band'] = True if wiggleOpts['variance_band'] == 'true' else False | |
| 445 | |
| 446 if 'min' in wiggleOpts and 'max' in wiggleOpts: | |
| 447 trackData['min_score'] = wiggleOpts['min'] | |
| 448 trackData['max_score'] = wiggleOpts['max'] | |
| 449 else: | |
| 450 trackData['autoscale'] = wiggleOpts.get('autoscale', 'local') | |
| 451 | |
| 452 self._add_track_json(trackData) | |
| 453 | |
| 454 def add_bam(self, data, trackData, bamOpts, bam_index=None, **kwargs): | |
| 455 dest = os.path.join('data', 'raw', trackData['label'] + '.bam') | |
| 456 cmd = ['ln', '-s', os.path.realpath(data), dest] | |
|
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457 self.subprocess_check_call(cmd) |
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458 |
| 3 | 459 cmd = ['ln', '-s', os.path.realpath(bam_index), dest + '.bai'] |
| 460 self.subprocess_check_call(cmd) | |
| 461 | |
| 462 trackData.update({ | |
|
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463 "urlTemplate": os.path.join('..', dest), |
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464 "type": "JBrowse/View/Track/Alignments2", |
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465 "storeClass": "JBrowse/Store/SeqFeature/BAM", |
| 3 | 466 }) |
| 467 | |
| 468 self._add_track_json(trackData) | |
| 469 | |
| 470 if bamOpts.get('auto_snp', 'false') == 'true': | |
| 471 trackData2 = copy.copy(trackData) | |
| 472 trackData2.update({ | |
|
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473 "type": "JBrowse/View/Track/SNPCoverage", |
| 3 | 474 "key": trackData['key'] + " - SNPs/Coverage", |
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475 "label": trackData['label'] + "_autosnp", |
| 3 | 476 }) |
| 477 self._add_track_json(trackData2) | |
|
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478 |
| 3 | 479 def add_vcf(self, data, trackData, vcfOpts={}, **kwargs): |
| 480 dest = os.path.join('data', 'raw', trackData['label'] + '.vcf') | |
|
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481 # ln? |
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482 cmd = ['ln', '-s', data, dest] |
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483 self.subprocess_check_call(cmd) |
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484 cmd = ['bgzip', dest] |
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485 self.subprocess_check_call(cmd) |
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486 cmd = ['tabix', '-p', 'vcf', dest + '.gz'] |
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487 self.subprocess_check_call(cmd) |
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488 |
| 3 | 489 trackData.update({ |
|
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490 "urlTemplate": os.path.join('..', dest + '.gz'), |
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491 "type": "JBrowse/View/Track/HTMLVariants", |
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492 "storeClass": "JBrowse/Store/SeqFeature/VCFTabix", |
| 3 | 493 }) |
| 494 self._add_track_json(trackData) | |
|
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495 |
| 3 | 496 def add_features(self, data, format, trackData, gffOpts, **kwargs): |
| 497 cmd = [ | |
| 498 'perl', self._jbrowse_bin('flatfile-to-json.pl'), | |
| 499 self.TN_TABLE.get(format, 'gff'), | |
| 500 data, | |
| 501 '--trackLabel', trackData['label'], | |
| 502 '--key', trackData['key'] | |
| 503 ] | |
|
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504 |
| 3 | 505 config = copy.copy(trackData) |
| 506 clientConfig = trackData['style'] | |
| 507 del config['style'] | |
|
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508 |
|
8
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509 if 'match' in gffOpts: |
|
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510 config['glyph'] = 'JBrowse/View/FeatureGlyph/Segments' |
| 3 | 511 cmd += ['--type', gffOpts['match']] |
|
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512 |
| 3 | 513 cmd += ['--clientConfig', json.dumps(clientConfig), |
|
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514 ] |
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515 |
|
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516 trackType = 'JBrowse/View/Track/CanvasFeatures' |
|
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517 if 'trackType' in gffOpts: |
|
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518 trackType = gffOpts['trackType'] |
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519 |
|
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520 if trackType == 'JBrowse/View/Track/CanvasFeatures': |
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521 if 'transcriptType' in gffOpts and gffOpts['transcriptType']: |
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522 config['transcriptType'] = gffOpts['transcriptType'] |
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523 if 'subParts' in gffOpts and gffOpts['subParts']: |
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524 config['subParts'] = gffOpts['subParts'] |
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525 if 'impliedUTRs' in gffOpts and gffOpts['impliedUTRs']: |
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526 config['impliedUTRs'] = gffOpts['impliedUTRs'] |
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527 |
|
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528 cmd += [ |
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529 '--trackType', gffOpts['trackType'] |
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530 ] |
|
1
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531 |
|
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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532 cmd.extend(['--config', json.dumps(config)]) |
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533 |
|
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534 self.subprocess_check_call(cmd) |
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535 |
|
8
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536 if gffOpts.get('index', 'false') == 'true': |
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537 self.tracksToIndex.append("%s" % trackData['label']) |
| 3 | 538 |
| 539 def process_annotations(self, track): | |
| 540 outputTrackConfig = { | |
| 541 'style': { | |
|
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542 'label': track['style'].get('label', 'description'), |
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543 'className': track['style'].get('className', 'feature'), |
| 3 | 544 'description': track['style'].get('description', ''), |
| 545 }, | |
| 546 'category': track['category'], | |
| 547 } | |
| 548 | |
| 549 for i, (dataset_path, dataset_ext, track_human_label) in enumerate(track['trackfiles']): | |
| 550 log.info('Processing %s / %s', track['category'], track_human_label) | |
| 551 outputTrackConfig['key'] = track_human_label | |
| 552 hashData = [dataset_path, track_human_label, track['category']] | |
|
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553 outputTrackConfig['label'] = hashlib.md5('|'.join(hashData).encode('utf-8')).hexdigest() + '_%s' % i |
| 3 | 554 |
| 555 # Colour parsing is complex due to different track types having | |
| 556 # different colour options. | |
| 557 colourOptions = self.cs.parse_colours(track['conf']['options'], track['format'], gff3=dataset_path) | |
| 558 # This used to be done with a dict.update() call, however that wiped out any previous style settings... | |
| 559 for key in colourOptions: | |
| 560 if key == 'style': | |
| 561 for subkey in colourOptions['style']: | |
| 562 outputTrackConfig['style'][subkey] = colourOptions['style'][subkey] | |
| 563 else: | |
| 564 outputTrackConfig[key] = colourOptions[key] | |
| 565 | |
|
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566 menus = self.cs.parse_menus(track['conf']['options']) |
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567 outputTrackConfig.update(menus) |
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568 |
|
5
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569 # import pprint; pprint.pprint(track) |
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570 # import sys; sys.exit() |
| 3 | 571 if dataset_ext in ('gff', 'gff3', 'bed'): |
| 572 self.add_features(dataset_path, dataset_ext, outputTrackConfig, | |
|
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573 track['conf']['options']['gff']) |
| 3 | 574 elif dataset_ext == 'bigwig': |
| 575 self.add_bigwig(dataset_path, outputTrackConfig, | |
| 576 track['conf']['options']['wiggle']) | |
| 577 elif dataset_ext == 'bam': | |
| 578 real_indexes = track['conf']['options']['pileup']['bam_indices']['bam_index'] | |
| 579 if not isinstance(real_indexes, list): | |
| 580 # <bam_indices> | |
| 581 # <bam_index>/path/to/a.bam.bai</bam_index> | |
| 582 # </bam_indices> | |
| 583 # | |
| 584 # The above will result in the 'bam_index' key containing a | |
| 585 # string. If there are two or more indices, the container | |
| 586 # becomes a list. Fun! | |
| 587 real_indexes = [real_indexes] | |
| 588 | |
| 589 self.add_bam(dataset_path, outputTrackConfig, | |
| 590 track['conf']['options']['pileup'], | |
| 591 bam_index=real_indexes[i]) | |
| 592 elif dataset_ext == 'blastxml': | |
| 593 self.add_blastxml(dataset_path, outputTrackConfig, track['conf']['options']['blast']) | |
| 594 elif dataset_ext == 'vcf': | |
| 595 self.add_vcf(dataset_path, outputTrackConfig) | |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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diff
changeset
|
596 |
|
5
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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changeset
|
597 # Return non-human label for use in other fields |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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598 yield outputTrackConfig['label'] |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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|
599 |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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changeset
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600 def add_final_data(self, data): |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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601 viz_data = {} |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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changeset
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602 if len(data['visibility']['default_on']) > 0: |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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changeset
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603 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
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changeset
|
604 |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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changeset
|
605 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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changeset
|
606 viz_data['alwaysOnTracks'] = ','.join(data['visibility']['always']) |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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changeset
|
607 |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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changeset
|
608 if len(data['visibility']['force']) > 0: |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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changeset
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609 viz_data['forceTracks'] = ','.join(data['visibility']['force']) |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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changeset
|
610 |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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changeset
|
611 generalData = {} |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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changeset
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612 if data['general']['aboutDescription'] is not None: |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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changeset
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613 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
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changeset
|
614 |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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changeset
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615 generalData['view'] = { |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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changeset
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616 'trackPadding': data['general']['trackPadding'] |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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617 } |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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changeset
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618 generalData['shareLink'] = (data['general']['shareLink'] == 'true') |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
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changeset
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619 generalData['show_tracklist'] = (data['general']['show_tracklist'] == 'true') |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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changeset
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620 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
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changeset
|
621 generalData['show_overview'] = (data['general']['show_overview'] == 'true') |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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diff
changeset
|
622 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
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diff
changeset
|
623 generalData['hideGenomeOptions'] = (data['general']['hideGenomeOptions'] == 'true') |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
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changeset
|
624 |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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changeset
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625 viz_data.update(generalData) |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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changeset
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626 self._add_json(viz_data) |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
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changeset
|
627 |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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628 def clone_jbrowse(self, jbrowse_dir, destination): |
| 3 | 629 """Clone a JBrowse directory into a destination directory. |
| 630 """ | |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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diff
changeset
|
631 # 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
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changeset
|
632 # unlike copytree |
| 3 | 633 cmd = ['cp', '-r', os.path.join(jbrowse_dir, '.'), destination] |
| 634 log.debug(' '.join(cmd)) | |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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635 subprocess.check_call(cmd) |
| 3 | 636 cmd = ['mkdir', '-p', os.path.join(destination, 'data', 'raw')] |
| 637 log.debug(' '.join(cmd)) | |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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diff
changeset
|
638 subprocess.check_call(cmd) |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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diff
changeset
|
639 |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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diff
changeset
|
640 # 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
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diff
changeset
|
641 # JBrowse releases come with some broken symlinks |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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changeset
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642 cmd = ['find', destination, '-type', 'l', '-xtype', 'l', '-exec', 'rm', "'{}'", '+'] |
| 3 | 643 log.debug(' '.join(cmd)) |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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diff
changeset
|
644 subprocess.check_call(cmd) |
|
0
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
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diff
changeset
|
645 |
|
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
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diff
changeset
|
646 |
|
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
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changeset
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647 if __name__ == '__main__': |
|
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
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changeset
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648 parser = argparse.ArgumentParser(description="", epilog="") |
|
10
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
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changeset
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649 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
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changeset
|
650 |
|
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
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changeset
|
651 parser.add_argument('--jbrowse', help='Folder containing a jbrowse release') |
|
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
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652 parser.add_argument('--outdir', help='Output directory', default='out') |
| 3 | 653 parser.add_argument('--standalone', help='Standalone mode includes a copy of JBrowse', action='store_true') |
|
0
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
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changeset
|
654 args = parser.parse_args() |
|
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
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changeset
|
655 |
| 3 | 656 tree = ET.parse(args.xml.name) |
| 657 root = tree.getroot() | |
| 658 | |
|
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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changeset
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659 jc = JbrowseConnector( |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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660 jbrowse=args.jbrowse, |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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661 outdir=args.outdir, |
| 3 | 662 genomes=[os.path.realpath(x.text) for x in root.findall('metadata/genomes/genome')], |
| 663 standalone=args.standalone, | |
| 664 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
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diff
changeset
|
665 ) |
|
0
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
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diff
changeset
|
666 |
|
5
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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changeset
|
667 extra_data = { |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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changeset
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668 'visibility': { |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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changeset
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669 'default_on': [], |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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|
670 'default_off': [], |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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671 'force': [], |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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672 'always': [], |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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673 }, |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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changeset
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674 'general': { |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
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675 '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
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changeset
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676 '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
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changeset
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677 '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
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diff
changeset
|
678 '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
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diff
changeset
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679 '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
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changeset
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680 'show_nav': root.find('metadata/general/show_nav').text, |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
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changeset
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681 'show_overview': root.find('metadata/general/show_overview').text, |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
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682 'show_menu': root.find('metadata/general/show_menu').text, |
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ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
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3
diff
changeset
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683 'hideGenomeOptions': root.find('metadata/general/hideGenomeOptions').text, |
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ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
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3
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changeset
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684 } |
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ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
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685 } |
| 3 | 686 for track in root.findall('tracks/track'): |
| 687 track_conf = {} | |
| 688 track_conf['trackfiles'] = [ | |
| 689 (os.path.realpath(x.attrib['path']), x.attrib['ext'], x.attrib['label']) | |
| 690 for x in track.findall('files/trackFile') | |
| 691 ] | |
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1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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692 |
| 3 | 693 track_conf['category'] = track.attrib['cat'] |
| 694 track_conf['format'] = track.attrib['format'] | |
| 695 try: | |
| 696 # Only pertains to gff3 + blastxml. TODO? | |
| 697 track_conf['style'] = {t.tag: t.text for t in track.find('options/style')} | |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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changeset
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698 except TypeError: |
| 3 | 699 track_conf['style'] = {} |
| 700 pass | |
| 701 track_conf['conf'] = etree_to_dict(track.find('options')) | |
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5
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
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702 keys = jc.process_annotations(track_conf) |
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ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
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703 |
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ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
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704 for key in keys: |
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ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
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705 extra_data['visibility'][track.attrib.get('visibility', 'default_off')].append(key) |
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ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
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706 |
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ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
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707 jc.add_final_data(extra_data) |
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8
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
5
diff
changeset
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708 jc.generate_names() |