Mercurial > repos > iuc > jbrowse
annotate jbrowse.py @ 11:4cbceec1d6b4 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 172014e3f03ea00dfd5fcd689e1246d001e82288
| author | iuc |
|---|---|
| date | Wed, 14 Dec 2016 09:19:48 -0500 |
| parents | 1a6d882d340d |
| children | db5fe5a3176a |
| 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
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1 #!/usr/bin/env python |
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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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2 import argparse |
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11
4cbceec1d6b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 172014e3f03ea00dfd5fcd689e1246d001e82288
iuc
parents:
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changeset
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3 import codecs |
| 3 | 4 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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5 import hashlib |
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8
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 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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changeset
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7 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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8 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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changeset
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9 import shutil |
| 3 | 10 import struct |
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8
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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11 import subprocess |
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1
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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12 import tempfile |
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8
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 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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14 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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15 |
| 3 | 16 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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17 |
| 3 | 18 logging.basicConfig(level=logging.INFO) |
| 19 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
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20 |
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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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21 |
| 3 | 22 class ColorScaling(object): |
| 23 | |
| 24 COLOR_FUNCTION_TEMPLATE = """ | |
| 25 function(feature, variableName, glyphObject, track) {{ | |
| 26 var score = {score}; | |
| 27 {opacity} | |
| 28 return 'rgba({red}, {green}, {blue}, ' + opacity + ')'; | |
| 29 }} | |
| 30 """ | |
| 31 | |
| 32 COLOR_FUNCTION_TEMPLATE_QUAL = """ | |
| 33 function(feature, variableName, glyphObject, track) {{ | |
| 34 var search_up = function self(sf, attr){{ | |
| 35 if(sf.get(attr) !== undefined){{ | |
| 36 return sf.get(attr); | |
| 37 }} | |
| 38 if(sf.parent() === undefined) {{ | |
| 39 return; | |
| 40 }}else{{ | |
| 41 return self(sf.parent(), attr); | |
| 42 }} | |
| 43 }}; | |
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0
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
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changeset
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44 |
| 3 | 45 var search_down = function self(sf, attr){{ |
| 46 if(sf.get(attr) !== undefined){{ | |
| 47 return sf.get(attr); | |
| 48 }} | |
| 49 if(sf.children() === undefined) {{ | |
| 50 return; | |
| 51 }}else{{ | |
| 52 var kids = sf.children(); | |
| 53 for(var child_idx in kids){{ | |
| 54 var x = self(kids[child_idx], attr); | |
| 55 if(x !== undefined){{ | |
| 56 return x; | |
| 57 }} | |
| 58 }} | |
| 59 return; | |
| 60 }} | |
| 61 }}; | |
| 62 | |
| 63 var color = ({user_spec_color} || search_up(feature, 'color') || search_down(feature, 'color') || {auto_gen_color}); | |
| 64 var score = (search_up(feature, 'score') || search_down(feature, 'score')); | |
| 65 {opacity} | |
| 66 var result = /^#?([a-f\d]{{2}})([a-f\d]{{2}})([a-f\d]{{2}})$/i.exec(color); | |
| 67 var red = parseInt(result[1], 16); | |
| 68 var green = parseInt(result[2], 16); | |
| 69 var blue = parseInt(result[3], 16); | |
| 70 if(isNaN(opacity) || opacity < 0){{ opacity = 0; }} | |
| 71 return 'rgba(' + red + ',' + green + ',' + blue + ',' + opacity + ')'; | |
| 72 }} | |
| 73 """ | |
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0
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
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74 |
| 3 | 75 OPACITY_MATH = { |
| 76 'linear': """ | |
| 77 var opacity = (score - ({min})) / (({max}) - ({min})); | |
| 78 """, | |
| 79 'logarithmic': """ | |
| 80 var opacity = (score - ({min})) / (({max}) - ({min})); | |
| 81 opacity = Math.log10(opacity) + Math.log10({max}); | |
| 82 """, | |
| 83 'blast': """ | |
| 84 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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85 if(score == 0.0) { |
| 3 | 86 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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87 } else{ |
| 3 | 88 opacity = (20 - Math.log10(score)) / 180; |
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8
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
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89 } |
| 3 | 90 """ |
| 91 } | |
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1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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changeset
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92 |
| 3 | 93 BREWER_COLOUR_IDX = 0 |
| 94 BREWER_COLOUR_SCHEMES = [ | |
| 95 (166, 206, 227), | |
| 96 (31, 120, 180), | |
| 97 (178, 223, 138), | |
| 98 (51, 160, 44), | |
| 99 (251, 154, 153), | |
| 100 (227, 26, 28), | |
| 101 (253, 191, 111), | |
| 102 (255, 127, 0), | |
| 103 (202, 178, 214), | |
| 104 (106, 61, 154), | |
| 105 (255, 255, 153), | |
| 106 (177, 89, 40), | |
| 107 (228, 26, 28), | |
| 108 (55, 126, 184), | |
| 109 (77, 175, 74), | |
| 110 (152, 78, 163), | |
| 111 (255, 127, 0), | |
| 112 ] | |
| 113 | |
| 114 BREWER_DIVERGING_PALLETES = { | |
| 115 'BrBg': ("#543005", "#003c30"), | |
| 116 'PiYg': ("#8e0152", "#276419"), | |
| 117 'PRGn': ("#40004b", "#00441b"), | |
| 118 'PuOr': ("#7f3b08", "#2d004b"), | |
| 119 'RdBu': ("#67001f", "#053061"), | |
| 120 'RdGy': ("#67001f", "#1a1a1a"), | |
| 121 'RdYlBu': ("#a50026", "#313695"), | |
| 122 'RdYlGn': ("#a50026", "#006837"), | |
| 123 'Spectral': ("#9e0142", "#5e4fa2"), | |
| 124 } | |
| 125 | |
| 126 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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127 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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128 |
| 3 | 129 def rgb_from_hex(self, hexstr): |
| 130 # http://stackoverflow.com/questions/4296249/how-do-i-convert-a-hex-triplet-to-an-rgb-tuple-and-back | |
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4cbceec1d6b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 172014e3f03ea00dfd5fcd689e1246d001e82288
iuc
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131 return struct.unpack('BBB', codecs.decode(hexstr, '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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132 |
| 3 | 133 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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134 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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135 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
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136 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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137 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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138 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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139 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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140 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
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141 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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142 |
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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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143 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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144 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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145 |
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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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146 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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147 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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148 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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149 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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150 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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151 |
| 3 | 152 def hex_from_rgb(self, r, g, b): |
| 153 return '#%02x%02x%02x' % (r, g, b) | |
| 154 | |
| 155 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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156 r, g, b = self.BREWER_COLOUR_SCHEMES[self.brewer_colour_idx % len(self.BREWER_COLOUR_SCHEMES)] |
| 3 | 157 self.brewer_colour_idx += 1 |
| 158 return r, g, b | |
| 159 | |
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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 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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161 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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162 |
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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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163 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
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164 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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165 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
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166 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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167 |
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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 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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169 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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170 '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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171 '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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172 '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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173 } |
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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 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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175 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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176 if 'content' in m: |
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177 tpl['content'] = m['content'] |
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178 if 'title' in m: |
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179 tpl['title'] = m['title'] |
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180 |
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181 trackConfig['menuTemplate'].append(tpl) |
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182 |
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183 return trackConfig |
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184 |
| 3 | 185 def parse_colours(self, track, trackFormat, gff3=None): |
| 186 # Wiggle tracks have a bicolor pallete | |
| 187 trackConfig = {'style': {}} | |
| 188 if trackFormat == 'wiggle': | |
| 189 | |
| 190 trackConfig['style']['pos_color'] = track['wiggle']['color_pos'] | |
| 191 trackConfig['style']['neg_color'] = track['wiggle']['color_neg'] | |
| 192 | |
| 193 if trackConfig['style']['pos_color'] == '__auto__': | |
| 194 trackConfig['style']['neg_color'] = self.hex_from_rgb(*self._get_colours()) | |
| 195 trackConfig['style']['pos_color'] = self.hex_from_rgb(*self._get_colours()) | |
| 196 | |
| 197 # Wiggle tracks can change colour at a specified place | |
| 198 bc_pivot = track['wiggle']['bicolor_pivot'] | |
| 199 if bc_pivot not in ('mean', 'zero'): | |
| 200 # The values are either one of those two strings | |
| 201 # or a number | |
| 202 bc_pivot = float(bc_pivot) | |
| 203 trackConfig['bicolor_pivot'] = bc_pivot | |
| 204 elif 'scaling' in track: | |
| 205 if track['scaling']['method'] == 'ignore': | |
| 206 if track['scaling']['scheme']['color'] != '__auto__': | |
| 207 trackConfig['style']['color'] = track['scaling']['scheme']['color'] | |
| 208 else: | |
| 209 trackConfig['style']['color'] = self.hex_from_rgb(*self._get_colours()) | |
| 210 else: | |
| 211 # Scored method | |
| 212 algo = track['scaling']['algo'] | |
| 213 # linear, logarithmic, blast | |
| 214 scales = track['scaling']['scales'] | |
| 215 # type __auto__, manual (min, max) | |
| 216 scheme = track['scaling']['scheme'] | |
| 217 # scheme -> (type (opacity), color) | |
| 218 # ================================== | |
| 219 # GENE CALLS OR BLAST | |
| 220 # ================================== | |
| 221 if trackFormat == 'blast': | |
| 222 red, green, blue = self._get_colours() | |
| 223 color_function = self.COLOR_FUNCTION_TEMPLATE.format(**{ | |
| 224 'score': "feature._parent.get('score')", | |
| 225 'opacity': self.OPACITY_MATH['blast'], | |
| 226 'red': red, | |
| 227 'green': green, | |
| 228 'blue': blue, | |
| 229 }) | |
| 230 trackConfig['style']['color'] = color_function.replace('\n', '') | |
| 231 elif trackFormat == 'gene_calls': | |
| 232 # Default values, based on GFF3 spec | |
| 233 min_val = 0 | |
| 234 max_val = 1000 | |
| 235 # Get min/max and build a scoring function since JBrowse doesn't | |
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236 if scales['type'] == 'automatic' or scales['type'] == '__auto__': |
| 3 | 237 min_val, max_val = self.min_max_gff(gff3) |
| 238 else: | |
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239 min_val = scales.get('min', 0) |
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240 max_val = scales.get('max', 1000) |
| 3 | 241 |
| 242 if scheme['color'] == '__auto__': | |
| 243 user_color = 'undefined' | |
| 244 auto_color = "'%s'" % self.hex_from_rgb(*self._get_colours()) | |
| 245 elif scheme['color'].startswith('#'): | |
| 246 user_color = "'%s'" % self.hex_from_rgb(*self.rgb_from_hex(scheme['color'][1:])) | |
| 247 auto_color = 'undefined' | |
| 248 else: | |
| 249 user_color = 'undefined' | |
| 250 auto_color = "'%s'" % self.hex_from_rgb(*self._get_colours()) | |
| 251 | |
| 252 color_function = self.COLOR_FUNCTION_TEMPLATE_QUAL.format(**{ | |
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253 'opacity': self.OPACITY_MATH[algo].format(**{'max': max_val, 'min': min_val}), |
| 3 | 254 'user_spec_color': user_color, |
| 255 'auto_gen_color': auto_color, | |
| 256 }) | |
| 257 | |
| 258 trackConfig['style']['color'] = color_function.replace('\n', '') | |
| 259 return trackConfig | |
| 260 | |
| 261 | |
| 262 def etree_to_dict(t): | |
| 263 d = {t.tag: {} if t.attrib else None} | |
| 264 children = list(t) | |
| 265 if children: | |
| 266 dd = defaultdict(list) | |
| 267 for dc in map(etree_to_dict, children): | |
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268 for k, v in dc.items(): |
| 3 | 269 dd[k].append(v) |
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270 d = {t.tag: {k: v[0] if len(v) == 1 else v for k, v in dd.items()}} |
| 3 | 271 if t.attrib: |
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272 d[t.tag].update(('@' + k, v) for k, v in t.attrib.items()) |
| 3 | 273 if t.text: |
| 274 text = t.text.strip() | |
| 275 if children or t.attrib: | |
| 276 if text: | |
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277 d[t.tag]['#text'] = text |
| 3 | 278 else: |
| 279 d[t.tag] = text | |
| 280 return d | |
| 281 | |
| 282 | |
| 283 # score comes from feature._parent.get('score') or feature.get('score') | |
| 284 | |
| 285 INSTALLED_TO = os.path.dirname(os.path.realpath(__file__)) | |
| 286 | |
| 287 | |
| 288 class JbrowseConnector(object): | |
| 289 | |
| 290 def __init__(self, jbrowse, outdir, genomes, standalone=False, gencode=1): | |
| 291 self.TN_TABLE = { | |
| 292 'gff3': '--gff', | |
| 293 'gff': '--gff', | |
| 294 'bed': '--bed', | |
| 295 'genbank': '--gbk', | |
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296 } |
| 3 | 297 |
| 298 self.cs = ColorScaling() | |
| 299 self.jbrowse = jbrowse | |
| 300 self.outdir = outdir | |
| 301 self.genome_paths = genomes | |
| 302 self.standalone = standalone | |
| 303 self.gencode = gencode | |
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304 self.tracksToIndex = [] |
| 3 | 305 |
| 306 if standalone: | |
| 307 self.clone_jbrowse(self.jbrowse, self.outdir) | |
| 308 else: | |
| 309 try: | |
| 310 os.makedirs(self.outdir) | |
| 311 except OSError: | |
| 312 # Ignore if the folder exists | |
| 313 pass | |
| 314 | |
| 315 self.process_genomes() | |
| 316 self.update_gencode() | |
| 317 | |
| 318 def update_gencode(self): | |
| 319 table = CodonTable.unambiguous_dna_by_id[int(self.gencode)] | |
| 320 trackList = os.path.join(self.outdir, 'data', 'trackList.json') | |
| 321 with open(trackList, 'r') as handle: | |
| 322 trackListData = json.load(handle) | |
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323 |
| 3 | 324 trackListData['tracks'][0].update({ |
| 325 'codonStarts': table.start_codons, | |
| 326 'codonStops': table.stop_codons, | |
| 327 'codonTable': table.forward_table, | |
| 328 }) | |
| 329 | |
| 330 with open(trackList, 'w') as handle: | |
| 331 json.dump(trackListData, handle, indent=2) | |
| 332 | |
| 333 def subprocess_check_call(self, command): | |
| 334 log.debug('cd %s && %s', self.outdir, ' '.join(command)) | |
| 335 subprocess.check_call(command, cwd=self.outdir) | |
| 336 | |
| 337 def _jbrowse_bin(self, command): | |
| 338 return os.path.realpath(os.path.join(self.jbrowse, 'bin', command)) | |
| 339 | |
| 340 def process_genomes(self): | |
| 341 for genome_path in self.genome_paths: | |
| 342 self.subprocess_check_call([ | |
| 343 'perl', self._jbrowse_bin('prepare-refseqs.pl'), | |
| 344 '--fasta', genome_path]) | |
| 345 | |
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346 def generate_names(self): |
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347 # Generate names |
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348 |
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349 args = [ |
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350 'perl', self._jbrowse_bin('generate-names.pl'), |
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351 '--hashBits', '16' |
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352 ] |
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353 |
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354 tracks = ','.join(self.tracksToIndex) |
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355 |
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356 if tracks: |
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357 args += ['--tracks', tracks] |
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358 else: |
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359 # No tracks to index, index only the refseq |
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360 args += ['--tracks', 'DNA'] |
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361 |
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362 self.subprocess_check_call(args) |
| 3 | 363 |
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364 def _add_json(self, json_data): |
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365 |
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366 cmd = [ |
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367 'perl', self._jbrowse_bin('add-json.pl'), |
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368 json.dumps(json_data), |
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369 os.path.join('data', 'trackList.json') |
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370 ] |
| 3 | 371 self.subprocess_check_call(cmd) |
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372 |
| 3 | 373 def _add_track_json(self, json_data): |
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374 if len(json_data) == 0: |
| 3 | 375 return |
| 376 | |
| 377 tmp = tempfile.NamedTemporaryFile(delete=False) | |
| 378 tmp.write(json.dumps(json_data)) | |
| 379 tmp.close() | |
| 380 cmd = ['perl', self._jbrowse_bin('add-track-json.pl'), tmp.name, | |
| 381 os.path.join('data', 'trackList.json')] | |
| 382 self.subprocess_check_call(cmd) | |
| 383 os.unlink(tmp.name) | |
| 384 | |
| 385 def _blastxml_to_gff3(self, xml, min_gap=10): | |
| 386 gff3_unrebased = tempfile.NamedTemporaryFile(delete=False) | |
| 387 cmd = ['python', os.path.join(INSTALLED_TO, 'blastxml_to_gapped_gff3.py'), | |
| 388 '--trim', '--trim_end', '--min_gap', str(min_gap), xml] | |
| 389 log.debug('cd %s && %s > %s', self.outdir, ' '.join(cmd), gff3_unrebased.name) | |
| 390 subprocess.check_call(cmd, cwd=self.outdir, stdout=gff3_unrebased) | |
| 391 gff3_unrebased.close() | |
| 392 return gff3_unrebased.name | |
| 393 | |
| 394 def add_blastxml(self, data, trackData, blastOpts, **kwargs): | |
| 395 gff3 = self._blastxml_to_gff3(data, min_gap=blastOpts['min_gap']) | |
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396 |
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397 if 'parent' in blastOpts and blastOpts['parent'] != 'None': |
| 3 | 398 gff3_rebased = tempfile.NamedTemporaryFile(delete=False) |
| 399 cmd = ['python', os.path.join(INSTALLED_TO, 'gff3_rebase.py')] | |
| 400 if blastOpts.get('protein', 'false') == 'true': | |
| 401 cmd.append('--protein2dna') | |
| 402 cmd.extend([os.path.realpath(blastOpts['parent']), gff3]) | |
| 403 log.debug('cd %s && %s > %s', self.outdir, ' '.join(cmd), gff3_rebased.name) | |
| 404 subprocess.check_call(cmd, cwd=self.outdir, stdout=gff3_rebased) | |
| 405 gff3_rebased.close() | |
| 406 | |
| 407 # Replace original gff3 file | |
| 408 shutil.copy(gff3_rebased.name, gff3) | |
| 409 os.unlink(gff3_rebased.name) | |
| 410 | |
| 411 config = { | |
| 412 'glyph': 'JBrowse/View/FeatureGlyph/Segments', | |
| 413 "category": trackData['category'], | |
| 414 } | |
| 415 | |
| 416 clientConfig = trackData['style'] | |
| 417 | |
| 418 cmd = ['perl', self._jbrowse_bin('flatfile-to-json.pl'), | |
| 419 '--gff', gff3, | |
| 420 '--trackLabel', trackData['label'], | |
| 421 '--key', trackData['key'], | |
| 422 '--clientConfig', json.dumps(clientConfig), | |
| 423 '--config', json.dumps(config), | |
| 424 '--trackType', 'JBrowse/View/Track/CanvasFeatures' | |
| 425 ] | |
| 426 | |
| 427 self.subprocess_check_call(cmd) | |
| 428 os.unlink(gff3) | |
| 429 | |
|
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430 if blastOpts.get('index', 'false') == 'true': |
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431 self.tracksToIndex.append("%s" % trackData['label']) |
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432 |
| 3 | 433 def add_bigwig(self, data, trackData, wiggleOpts, **kwargs): |
| 434 dest = os.path.join('data', 'raw', trackData['label'] + '.bw') | |
| 435 cmd = ['ln', data, dest] | |
|
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436 self.subprocess_check_call(cmd) |
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437 |
| 3 | 438 trackData.update({ |
| 439 "urlTemplate": os.path.join('..', dest), | |
| 440 "storeClass": "JBrowse/Store/SeqFeature/BigWig", | |
| 441 "type": "JBrowse/View/Track/Wiggle/Density", | |
| 442 }) | |
| 443 | |
| 444 trackData['type'] = wiggleOpts['type'] | |
| 445 trackData['variance_band'] = True if wiggleOpts['variance_band'] == 'true' else False | |
| 446 | |
| 447 if 'min' in wiggleOpts and 'max' in wiggleOpts: | |
| 448 trackData['min_score'] = wiggleOpts['min'] | |
| 449 trackData['max_score'] = wiggleOpts['max'] | |
| 450 else: | |
| 451 trackData['autoscale'] = wiggleOpts.get('autoscale', 'local') | |
| 452 | |
| 453 self._add_track_json(trackData) | |
| 454 | |
| 455 def add_bam(self, data, trackData, bamOpts, bam_index=None, **kwargs): | |
| 456 dest = os.path.join('data', 'raw', trackData['label'] + '.bam') | |
| 457 cmd = ['ln', '-s', os.path.realpath(data), dest] | |
|
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458 self.subprocess_check_call(cmd) |
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459 |
| 3 | 460 cmd = ['ln', '-s', os.path.realpath(bam_index), dest + '.bai'] |
| 461 self.subprocess_check_call(cmd) | |
| 462 | |
| 463 trackData.update({ | |
|
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464 "urlTemplate": os.path.join('..', dest), |
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465 "type": "JBrowse/View/Track/Alignments2", |
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466 "storeClass": "JBrowse/Store/SeqFeature/BAM", |
| 3 | 467 }) |
| 468 | |
| 469 self._add_track_json(trackData) | |
| 470 | |
| 471 if bamOpts.get('auto_snp', 'false') == 'true': | |
| 472 trackData2 = copy.copy(trackData) | |
| 473 trackData2.update({ | |
|
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474 "type": "JBrowse/View/Track/SNPCoverage", |
| 3 | 475 "key": trackData['key'] + " - SNPs/Coverage", |
|
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476 "label": trackData['label'] + "_autosnp", |
| 3 | 477 }) |
| 478 self._add_track_json(trackData2) | |
|
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479 |
| 3 | 480 def add_vcf(self, data, trackData, vcfOpts={}, **kwargs): |
| 481 dest = os.path.join('data', 'raw', trackData['label'] + '.vcf') | |
|
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482 # ln? |
|
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483 cmd = ['ln', '-s', data, dest] |
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484 self.subprocess_check_call(cmd) |
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485 cmd = ['bgzip', dest] |
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486 self.subprocess_check_call(cmd) |
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487 cmd = ['tabix', '-p', 'vcf', dest + '.gz'] |
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488 self.subprocess_check_call(cmd) |
|
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489 |
| 3 | 490 trackData.update({ |
|
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491 "urlTemplate": os.path.join('..', dest + '.gz'), |
|
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492 "type": "JBrowse/View/Track/HTMLVariants", |
|
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493 "storeClass": "JBrowse/Store/SeqFeature/VCFTabix", |
| 3 | 494 }) |
| 495 self._add_track_json(trackData) | |
|
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496 |
| 3 | 497 def add_features(self, data, format, trackData, gffOpts, **kwargs): |
| 498 cmd = [ | |
| 499 'perl', self._jbrowse_bin('flatfile-to-json.pl'), | |
| 500 self.TN_TABLE.get(format, 'gff'), | |
| 501 data, | |
| 502 '--trackLabel', trackData['label'], | |
| 503 '--key', trackData['key'] | |
| 504 ] | |
|
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505 |
| 3 | 506 config = copy.copy(trackData) |
| 507 clientConfig = trackData['style'] | |
| 508 del config['style'] | |
|
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509 |
|
8
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510 if 'match' in gffOpts: |
|
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511 config['glyph'] = 'JBrowse/View/FeatureGlyph/Segments' |
| 3 | 512 cmd += ['--type', gffOpts['match']] |
|
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513 |
| 3 | 514 cmd += ['--clientConfig', json.dumps(clientConfig), |
|
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515 ] |
|
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516 |
|
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517 trackType = 'JBrowse/View/Track/CanvasFeatures' |
|
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518 if 'trackType' in gffOpts: |
|
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519 trackType = gffOpts['trackType'] |
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520 |
|
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521 if trackType == 'JBrowse/View/Track/CanvasFeatures': |
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522 if 'transcriptType' in gffOpts and gffOpts['transcriptType']: |
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523 config['transcriptType'] = gffOpts['transcriptType'] |
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524 if 'subParts' in gffOpts and gffOpts['subParts']: |
|
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525 config['subParts'] = gffOpts['subParts'] |
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526 if 'impliedUTRs' in gffOpts and gffOpts['impliedUTRs']: |
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527 config['impliedUTRs'] = gffOpts['impliedUTRs'] |
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528 |
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529 cmd += [ |
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530 '--trackType', gffOpts['trackType'] |
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531 ] |
|
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532 |
|
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533 cmd.extend(['--config', json.dumps(config)]) |
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534 |
|
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535 self.subprocess_check_call(cmd) |
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536 |
|
8
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537 if gffOpts.get('index', 'false') == 'true': |
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538 self.tracksToIndex.append("%s" % trackData['label']) |
| 3 | 539 |
| 540 def process_annotations(self, track): | |
| 541 outputTrackConfig = { | |
| 542 'style': { | |
|
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543 'label': track['style'].get('label', 'description'), |
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544 'className': track['style'].get('className', 'feature'), |
| 3 | 545 'description': track['style'].get('description', ''), |
| 546 }, | |
| 547 'category': track['category'], | |
| 548 } | |
| 549 | |
| 550 for i, (dataset_path, dataset_ext, track_human_label) in enumerate(track['trackfiles']): | |
| 551 log.info('Processing %s / %s', track['category'], track_human_label) | |
| 552 outputTrackConfig['key'] = track_human_label | |
| 553 hashData = [dataset_path, track_human_label, track['category']] | |
|
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554 outputTrackConfig['label'] = hashlib.md5('|'.join(hashData).encode('utf-8')).hexdigest() + '_%s' % i |
| 3 | 555 |
| 556 # Colour parsing is complex due to different track types having | |
| 557 # different colour options. | |
| 558 colourOptions = self.cs.parse_colours(track['conf']['options'], track['format'], gff3=dataset_path) | |
| 559 # This used to be done with a dict.update() call, however that wiped out any previous style settings... | |
| 560 for key in colourOptions: | |
| 561 if key == 'style': | |
| 562 for subkey in colourOptions['style']: | |
| 563 outputTrackConfig['style'][subkey] = colourOptions['style'][subkey] | |
| 564 else: | |
| 565 outputTrackConfig[key] = colourOptions[key] | |
| 566 | |
|
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567 menus = self.cs.parse_menus(track['conf']['options']) |
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568 outputTrackConfig.update(menus) |
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569 |
|
5
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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570 # import pprint; pprint.pprint(track) |
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571 # import sys; sys.exit() |
| 3 | 572 if dataset_ext in ('gff', 'gff3', 'bed'): |
| 573 self.add_features(dataset_path, dataset_ext, outputTrackConfig, | |
|
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574 track['conf']['options']['gff']) |
| 3 | 575 elif dataset_ext == 'bigwig': |
| 576 self.add_bigwig(dataset_path, outputTrackConfig, | |
| 577 track['conf']['options']['wiggle']) | |
| 578 elif dataset_ext == 'bam': | |
| 579 real_indexes = track['conf']['options']['pileup']['bam_indices']['bam_index'] | |
| 580 if not isinstance(real_indexes, list): | |
| 581 # <bam_indices> | |
| 582 # <bam_index>/path/to/a.bam.bai</bam_index> | |
| 583 # </bam_indices> | |
| 584 # | |
| 585 # The above will result in the 'bam_index' key containing a | |
| 586 # string. If there are two or more indices, the container | |
| 587 # becomes a list. Fun! | |
| 588 real_indexes = [real_indexes] | |
| 589 | |
| 590 self.add_bam(dataset_path, outputTrackConfig, | |
| 591 track['conf']['options']['pileup'], | |
| 592 bam_index=real_indexes[i]) | |
| 593 elif dataset_ext == 'blastxml': | |
| 594 self.add_blastxml(dataset_path, outputTrackConfig, track['conf']['options']['blast']) | |
| 595 elif dataset_ext == 'vcf': | |
| 596 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
|
597 |
|
5
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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changeset
|
598 # 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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changeset
|
599 yield outputTrackConfig['label'] |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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changeset
|
600 |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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changeset
|
601 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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602 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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603 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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604 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
|
605 |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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changeset
|
606 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
|
607 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
|
608 |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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changeset
|
609 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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610 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
|
611 |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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changeset
|
612 generalData = {} |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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changeset
|
613 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
|
614 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
|
615 |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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changeset
|
616 generalData['view'] = { |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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changeset
|
617 '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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changeset
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618 } |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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changeset
|
619 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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diff
changeset
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620 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
|
621 generalData['show_nav'] = (data['general']['show_nav'] == 'true') |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
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diff
changeset
|
622 generalData['show_overview'] = (data['general']['show_overview'] == 'true') |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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parents:
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diff
changeset
|
623 generalData['show_menu'] = (data['general']['show_menu'] == 'true') |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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diff
changeset
|
624 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
|
625 |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
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changeset
|
626 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
|
627 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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diff
changeset
|
628 |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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changeset
|
629 def clone_jbrowse(self, jbrowse_dir, destination): |
| 3 | 630 """Clone a JBrowse directory into a destination directory. |
| 631 """ | |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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diff
changeset
|
632 # 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
|
633 # unlike copytree |
| 3 | 634 cmd = ['cp', '-r', os.path.join(jbrowse_dir, '.'), destination] |
| 635 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
|
636 subprocess.check_call(cmd) |
| 3 | 637 cmd = ['mkdir', '-p', os.path.join(destination, 'data', 'raw')] |
| 638 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
|
639 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
|
640 |
|
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 # 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
|
642 # 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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diff
changeset
|
643 cmd = ['find', destination, '-type', 'l', '-xtype', 'l', '-exec', 'rm', "'{}'", '+'] |
| 3 | 644 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
|
645 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
|
646 |
|
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
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changeset
|
647 |
|
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
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changeset
|
648 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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649 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
|
650 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
|
651 |
|
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
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changeset
|
652 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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653 parser.add_argument('--outdir', help='Output directory', default='out') |
| 3 | 654 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
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655 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
|
656 |
| 3 | 657 tree = ET.parse(args.xml.name) |
| 658 root = tree.getroot() | |
| 659 | |
|
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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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660 jc = JbrowseConnector( |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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661 jbrowse=args.jbrowse, |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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662 outdir=args.outdir, |
| 3 | 663 genomes=[os.path.realpath(x.text) for x in root.findall('metadata/genomes/genome')], |
| 664 standalone=args.standalone, | |
| 665 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
|
666 ) |
|
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
|
667 |
|
5
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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changeset
|
668 extra_data = { |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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changeset
|
669 'visibility': { |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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670 'default_on': [], |
|
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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671 'default_off': [], |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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|
672 'force': [], |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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673 'always': [], |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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674 }, |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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changeset
|
675 'general': { |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
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676 '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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677 '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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diff
changeset
|
678 '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
|
679 'aboutDescription': root.find('metadata/general/aboutDescription').text, |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
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diff
changeset
|
680 'show_tracklist': root.find('metadata/general/show_tracklist').text, |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
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diff
changeset
|
681 '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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682 'show_overview': root.find('metadata/general/show_overview').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 '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
parents:
3
diff
changeset
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684 '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
diff
changeset
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685 } |
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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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changeset
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686 } |
| 3 | 687 for track in root.findall('tracks/track'): |
| 688 track_conf = {} | |
| 689 track_conf['trackfiles'] = [ | |
| 690 (os.path.realpath(x.attrib['path']), x.attrib['ext'], x.attrib['label']) | |
| 691 for x in track.findall('files/trackFile') | |
| 692 ] | |
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1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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693 |
| 3 | 694 track_conf['category'] = track.attrib['cat'] |
| 695 track_conf['format'] = track.attrib['format'] | |
| 696 try: | |
| 697 # Only pertains to gff3 + blastxml. TODO? | |
| 698 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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diff
changeset
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699 except TypeError: |
| 3 | 700 track_conf['style'] = {} |
| 701 pass | |
| 702 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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703 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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704 |
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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 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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706 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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707 |
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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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708 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
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5
diff
changeset
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709 jc.generate_names() |