Mercurial > repos > fubar > jbrowse2

annotate abjbrowse2.py @ 14:7c2e28e144f3 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
author fubar
date Mon, 22 Jan 2024 12:05:09 +0000
parents 1d86925dbb4c
children
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1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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1 #!/usr/bin/env python
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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2 import argparse
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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3 import binascii
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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4 import datetime
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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5 import hashlib
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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6 import json
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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7 import logging
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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8 import os
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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9 import re
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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10 import shutil
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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11 import struct
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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12 import subprocess
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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13 import tempfile
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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14 import xml.etree.ElementTree as ET
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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15 from collections import defaultdict
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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17 logging.basicConfig(level=logging.INFO)
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18 log = logging.getLogger("jbrowse")
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19 TODAY = datetime.datetime.now().strftime("%Y-%m-%d")
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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20 GALAXY_INFRASTRUCTURE_URL = None
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23 class ColorScaling(object):
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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24
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25 COLOR_FUNCTION_TEMPLATE = """
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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26 function(feature, variableName, glyphObject, track) {{
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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27 var score = {score};
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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28 {opacity}
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29 return 'rgba({red}, {green}, {blue}, ' + opacity + ')';
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30 }}
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31 """
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32
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33 COLOR_FUNCTION_TEMPLATE_QUAL = r"""
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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34 function(feature, variableName, glyphObject, track) {{
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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35 var search_up = function self(sf, attr){{
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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36 if(sf.get(attr) !== undefined){{
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37 return sf.get(attr);
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38 }}
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39 if(sf.parent() === undefined) {{
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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40 return;
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41 }}else{{
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42 return self(sf.parent(), attr);
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43 }}
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44 }};
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45
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46 var search_down = function self(sf, attr){{
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47 if(sf.get(attr) !== undefined){{
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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48 return sf.get(attr);
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49 }}
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50 if(sf.children() === undefined) {{
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51 return;
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52 }}else{{
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53 var kids = sf.children();
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54 for(var child_idx in kids){{
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55 var x = self(kids[child_idx], attr);
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56 if(x !== undefined){{
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57 return x;
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58 }}
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59 }}
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60 return;
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61 }}
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62 }};
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63
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64 var color = ({user_spec_color} || search_up(feature, 'color') || search_down(feature, 'color') || {auto_gen_color});
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65 var score = (search_up(feature, 'score') || search_down(feature, 'score'));
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66 {opacity}
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67 if(score === undefined){{ opacity = 1; }}
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68 var result = /^#?([a-f\d]{{2}})([a-f\d]{{2}})([a-f\d]{{2}})$/i.exec(color);
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69 var red = parseInt(result[1], 16);
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70 var green = parseInt(result[2], 16);
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71 var blue = parseInt(result[3], 16);
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72 if(isNaN(opacity) || opacity < 0){{ opacity = 0; }}
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73 return 'rgba(' + red + ',' + green + ',' + blue + ',' + opacity + ')';
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74 }}
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75 """
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76
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77 OPACITY_MATH = {
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78 "linear": """
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79 var opacity = (score - ({min})) / (({max}) - ({min}));
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80 """,
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81 "logarithmic": """
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82 var opacity = Math.log10(score - ({min})) / Math.log10(({max}) - ({min}));
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83 """,
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84 "blast": """
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85 var opacity = 0;
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diff changeset
86 if(score == 0.0) {{
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
87 opacity = 1;
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
88 }} else {{
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
89 opacity = (20 - Math.log10(score)) / 180;
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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90 }}
14
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diff changeset
91 """,
13
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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92 }
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diff changeset
93
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94 BREWER_COLOUR_IDX = 0
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
95 BREWER_COLOUR_SCHEMES = [
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
96 (166, 206, 227),
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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parents:
diff changeset
97 (31, 120, 180),
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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parents:
diff changeset
98 (178, 223, 138),
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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parents:
diff changeset
99 (51, 160, 44),
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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parents:
diff changeset
100 (251, 154, 153),
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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parents:
diff changeset
101 (227, 26, 28),
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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parents:
diff changeset
102 (253, 191, 111),
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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parents:
diff changeset
103 (255, 127, 0),
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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parents:
diff changeset
104 (202, 178, 214),
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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parents:
diff changeset
105 (106, 61, 154),
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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parents:
diff changeset
106 (255, 255, 153),
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
107 (177, 89, 40),
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
108 (228, 26, 28),
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
109 (55, 126, 184),
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
110 (77, 175, 74),
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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parents:
diff changeset
111 (152, 78, 163),
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
112 (255, 127, 0),
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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113 ]
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114
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115 BREWER_DIVERGING_PALLETES = {
14
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116 "BrBg": ("#543005", "#003c30"),
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117 "PiYg": ("#8e0152", "#276419"),
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118 "PRGn": ("#40004b", "#00441b"),
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119 "PuOr": ("#7f3b08", "#2d004b"),
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120 "RdBu": ("#67001f", "#053061"),
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121 "RdGy": ("#67001f", "#1a1a1a"),
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122 "RdYlBu": ("#a50026", "#313695"),
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123 "RdYlGn": ("#a50026", "#006837"),
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124 "Spectral": ("#9e0142", "#5e4fa2"),
13
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125 }
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126
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127 def __init__(self):
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128 self.brewer_colour_idx = 0
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129
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130 def rgb_from_hex(self, hexstr):
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131 # http://stackoverflow.com/questions/4296249/how-do-i-convert-a-hex-triplet-to-an-rgb-tuple-and-back
14
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132 return struct.unpack("BBB", binascii.unhexlify(hexstr))
13
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133
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134 def min_max_gff(self, gff_file):
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135 min_val = None
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136 max_val = None
14
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137 with open(gff_file, "r") as handle:
13
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138 for line in handle:
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139 try:
14
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140 value = float(line.split("\t")[5])
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141 min_val = min(value, (min_val or value))
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142 max_val = max(value, (max_val or value))
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143
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144 if value < min_val:
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145 min_val = value
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146
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147 if value > max_val:
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148 max_val = value
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149 except Exception:
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150 pass
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151 return min_val, max_val
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152
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153 def hex_from_rgb(self, r, g, b):
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154 return "#%02x%02x%02x" % (r, g, b)
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155
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156 def _get_colours(self):
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157 r, g, b = self.BREWER_COLOUR_SCHEMES[
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158 self.brewer_colour_idx % len(self.BREWER_COLOUR_SCHEMES)
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159 ]
13
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160 self.brewer_colour_idx += 1
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161 return r, g, b
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162
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163 def parse_menus(self, track):
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164 trackConfig = {"menuTemplate": [{}, {}, {}, {}]}
13
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165
14
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166 if "menu" in track["menus"]:
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167 menu_list = [track["menus"]["menu"]]
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168 if isinstance(track["menus"]["menu"], list):
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169 menu_list = track["menus"]["menu"]
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170
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171 for m in menu_list:
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172 tpl = {
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173 "action": m["action"],
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174 "label": m.get("label", "{name}"),
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175 "iconClass": m.get("iconClass", "dijitIconBookmark"),
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176 }
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177 if "url" in m:
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178 tpl["url"] = m["url"]
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179 if "content" in m:
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180 tpl["content"] = m["content"]
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181 if "title" in m:
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182 tpl["title"] = m["title"]
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183
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184 trackConfig["menuTemplate"].append(tpl)
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185
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186 return trackConfig
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187
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188 def parse_colours(self, track, trackFormat, gff3=None):
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189 # Wiggle tracks have a bicolor pallete
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190 trackConfig = {"style": {}}
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191 if trackFormat == "wiggle":
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192
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193 trackConfig["style"]["pos_color"] = track["wiggle"]["color_pos"]
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194 trackConfig["style"]["neg_color"] = track["wiggle"]["color_neg"]
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195
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196 if trackConfig["style"]["pos_color"] == "__auto__":
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197 trackConfig["style"]["neg_color"] = self.hex_from_rgb(
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198 *self._get_colours()
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199 )
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200 trackConfig["style"]["pos_color"] = self.hex_from_rgb(
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201 *self._get_colours()
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202 )
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203
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204 # Wiggle tracks can change colour at a specified place
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205 bc_pivot = track["wiggle"]["bicolor_pivot"]
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206 if bc_pivot not in ("mean", "zero"):
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207 # The values are either one of those two strings
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208 # or a number
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209 bc_pivot = float(bc_pivot)
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210 trackConfig["bicolor_pivot"] = bc_pivot
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211 elif "scaling" in track:
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212 if track["scaling"]["method"] == "ignore":
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213 if track["scaling"]["scheme"]["color"] != "__auto__":
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214 trackConfig["style"]["color"] = track["scaling"]["scheme"]["color"]
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215 else:
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216 trackConfig["style"]["color"] = self.hex_from_rgb(
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217 *self._get_colours()
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218 )
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219 else:
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220 # Scored method
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221 algo = track["scaling"]["algo"]
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222 # linear, logarithmic, blast
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223 scales = track["scaling"]["scales"]
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224 # type __auto__, manual (min, max)
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225 scheme = track["scaling"]["scheme"]
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226 # scheme -> (type (opacity), color)
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227 # ==================================
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228 # GENE CALLS OR BLAST
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229 # ==================================
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230 if trackFormat == "blast":
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231 red, green, blue = self._get_colours()
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232 color_function = self.COLOR_FUNCTION_TEMPLATE.format(
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233 **{
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234 "score": "feature._parent.get('score')",
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235 "opacity": self.OPACITY_MATH["blast"],
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236 "red": red,
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237 "green": green,
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238 "blue": blue,
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239 }
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240 )
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241 trackConfig["style"]["color"] = color_function.replace("\n", "")
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242 elif trackFormat == "gene_calls":
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243 # Default values, based on GFF3 spec
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244 min_val = 0
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245 max_val = 1000
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246 # Get min/max and build a scoring function since JBrowse doesn't
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247 if scales["type"] == "automatic" or scales["type"] == "__auto__":
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248 min_val, max_val = self.min_max_gff(gff3)
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249 else:
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250 min_val = scales.get("min", 0)
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251 max_val = scales.get("max", 1000)
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252
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253 if scheme["color"] == "__auto__":
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254 user_color = "undefined"
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255 auto_color = "'%s'" % self.hex_from_rgb(*self._get_colours())
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256 elif scheme["color"].startswith("#"):
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257 user_color = "'%s'" % self.hex_from_rgb(
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258 *self.rgb_from_hex(scheme["color"][1:])
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259 )
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260 auto_color = "undefined"
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261 else:
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262 user_color = "undefined"
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263 auto_color = "'%s'" % self.hex_from_rgb(*self._get_colours())
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264
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265 color_function = self.COLOR_FUNCTION_TEMPLATE_QUAL.format(
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266 **{
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267 "opacity": self.OPACITY_MATH[algo].format(
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268 **{"max": max_val, "min": min_val}
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269 ),
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270 "user_spec_color": user_color,
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271 "auto_gen_color": auto_color,
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272 }
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273 )
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274
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275 trackConfig["style"]["color"] = color_function.replace("\n", "")
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276 return trackConfig
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277
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278
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279 def etree_to_dict(t):
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280 if t is None:
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281 return {}
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282
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283 d = {t.tag: {} if t.attrib else None}
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284 children = list(t)
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285 if children:
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286 dd = defaultdict(list)
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287 for dc in map(etree_to_dict, children):
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288 for k, v in dc.items():
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289 dd[k].append(v)
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290 d = {t.tag: {k: v[0] if len(v) == 1 else v for k, v in dd.items()}}
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291 if t.attrib:
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292 d[t.tag].update(("@" + k, v) for k, v in t.attrib.items())
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293 if t.text:
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294 text = t.text.strip()
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295 if children or t.attrib:
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296 if text:
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297 d[t.tag]["#text"] = text
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298 else:
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299 d[t.tag] = text
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300 return d
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301
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302
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303 # score comes from feature._parent.get('score') or feature.get('score')
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304
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305 INSTALLED_TO = os.path.dirname(os.path.realpath(__file__))
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306
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307
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308 def metadata_from_node(node):
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309 metadata = {}
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310 try:
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311 if len(node.findall("dataset")) != 1:
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312 # exit early
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313 return metadata
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314 except Exception:
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315 return {}
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316
14
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317 for (key, value) in node.findall("dataset")[0].attrib.items():
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318 metadata["dataset_%s" % key] = value
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319
14
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320 for (key, value) in node.findall("history")[0].attrib.items():
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321 metadata["history_%s" % key] = value
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322
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323 for (key, value) in node.findall("metadata")[0].attrib.items():
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324 metadata["metadata_%s" % key] = value
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325
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326 for (key, value) in node.findall("tool")[0].attrib.items():
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327 metadata["tool_%s" % key] = value
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328
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329 # Additional Mappings applied:
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330 metadata[
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331 "dataset_edam_format"
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332 ] = '<a target="_blank" href="http://edamontology.org/{0}">{1}</a>'.format(
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333 metadata["dataset_edam_format"], metadata["dataset_file_ext"]
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334 )
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335 metadata["history_user_email"] = '<a href="mailto:{0}">{0}</a>'.format(
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336 metadata["history_user_email"]
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337 )
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338 metadata[
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339 "history_display_name"
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340 ] = '<a target="_blank" href="{galaxy}/history/view/{encoded_hist_id}">{hist_name}</a>'.format(
13
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341 galaxy=GALAXY_INFRASTRUCTURE_URL,
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342 encoded_hist_id=metadata["history_id"],
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343 hist_name=metadata["history_display_name"],
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344 )
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345 metadata[
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346 "tool_tool"
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347 ] = '<a target="_blank" href="{galaxy}/datasets/{encoded_id}/show_params">{tool_id}</a>'.format(
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348 galaxy=GALAXY_INFRASTRUCTURE_URL,
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349 encoded_id=metadata["dataset_id"],
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350 tool_id=metadata["tool_tool_id"],
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351 # tool_version=metadata['tool_tool_version'],
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352 )
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353 return metadata
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354
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355
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356 class JbrowseConnector(object):
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357 def __init__(self, jbrowse, outdir, genomes):
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358 self.cs = ColorScaling()
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359 self.jbrowse = jbrowse
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360 self.outdir = outdir
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361 self.genome_paths = genomes
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362 self.tracksToIndex = []
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363
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364 # This is the id of the current assembly
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365 self.assembly_ids = {}
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366 self.current_assembly_id = []
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367
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368 # If upgrading, look at the existing data
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369 self.check_existing(self.outdir)
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370
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371 self.clone_jbrowse(self.jbrowse, self.outdir)
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372
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373 self.process_genomes()
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374
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375 def subprocess_check_call(self, command, output=None):
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376 if output:
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377 log.debug("cd %s && %s > %s", self.outdir, " ".join(command), output)
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378 subprocess.check_call(command, cwd=self.outdir, stdout=output)
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379 else:
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380 log.debug("cd %s && %s", self.outdir, " ".join(command))
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381 subprocess.check_call(command, cwd=self.outdir)
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382
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383 def subprocess_popen(self, command):
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384 log.debug("cd %s && %s", self.outdir, command)
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385 p = subprocess.Popen(
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386 command,
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387 shell=True,
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388 stdin=subprocess.PIPE,
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389 stdout=subprocess.PIPE,
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390 stderr=subprocess.PIPE,
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391 )
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392 output, err = p.communicate()
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393 retcode = p.returncode
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394 if retcode != 0:
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395 log.error("cd %s && %s", self.outdir, command)
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396 log.error(output)
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397 log.error(err)
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398 raise RuntimeError("Command failed with exit code %s" % (retcode))
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399
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400 def subprocess_check_output(self, command):
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401 log.debug("cd %s && %s", self.outdir, " ".join(command))
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402 return subprocess.check_output(command, cwd=self.outdir)
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403
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404 def symlink_or_copy(self, src, dest):
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405 if "GALAXY_JBROWSE_SYMLINKS" in os.environ and bool(
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406 os.environ["GALAXY_JBROWSE_SYMLINKS"]
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407 ):
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408 cmd = ["ln", "-s", src, dest]
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409 else:
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410 cmd = ["cp", src, dest]
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411
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412 return self.subprocess_check_call(cmd)
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413
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414 def symlink_or_copy_load_action(self):
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415 if "GALAXY_JBROWSE_SYMLINKS" in os.environ and bool(
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416 os.environ["GALAXY_JBROWSE_SYMLINKS"]
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417 ):
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418 return "symlink"
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419 else:
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420 return "copy"
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421
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422 def check_existing(self, destination):
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423 existing = os.path.join(destination, "data", "config.json")
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424 if os.path.exists(existing):
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425 with open(existing, "r") as existing_conf:
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426 conf = json.load(existing_conf)
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427 if "assemblies" in conf:
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428 for assembly in conf["assemblies"]:
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diff changeset
429 if "name" in assembly:
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430 self.assembly_ids[assembly["name"]] = None
13
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431
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432 def process_genomes(self):
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433 for genome_node in self.genome_paths:
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434 # We only expect one input genome per run. This for loop is just
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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435 # easier to write than the alternative / catches any possible
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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436 # issues.
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437 self.add_assembly(genome_node["path"], genome_node["label"])
13
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438
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439 def add_assembly(self, path, label, default=True):
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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440 # Find a non-existing filename for the new genome
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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441 # (to avoid colision when upgrading an existing instance)
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442 rel_seq_path = os.path.join("data", "assembly")
13
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443 seq_path = os.path.join(self.outdir, rel_seq_path)
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444 fn_try = 1
14
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diff changeset
445 while (
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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446 os.path.exists(seq_path + ".fasta")
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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447 or os.path.exists(seq_path + ".fasta.gz")
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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448 or os.path.exists(seq_path + ".fasta.gz.fai")
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449 or os.path.exists(seq_path + ".fasta.gz.gzi")
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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450 ):
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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451 rel_seq_path = os.path.join("data", "assembly%s" % fn_try)
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452 seq_path = os.path.join(self.outdir, rel_seq_path)
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453 fn_try += 1
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454
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455 # Find a non-existing label for the new genome
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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456 # (to avoid colision when upgrading an existing instance)
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457 lab_try = 1
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458 uniq_label = label
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459 while uniq_label in self.assembly_ids:
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460 uniq_label = label + str(lab_try)
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461 lab_try += 1
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462
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463 # Find a default scaffold to display
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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464 # TODO this may not be necessary in the future, see https://github.com/GMOD/jbrowse-components/issues/2708
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465 with open(path, "r") as fa_handle:
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466 fa_header = fa_handle.readline()[1:].strip().split(" ")[0]
13
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467
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468 self.assembly_ids[uniq_label] = fa_header
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469 if default:
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470 self.current_assembly_id = uniq_label
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471
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diff changeset
472 copied_genome = seq_path + ".fasta"
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473 shutil.copy(path, copied_genome)
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474
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475 # Compress with bgzip
14
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diff changeset
476 cmd = ["bgzip", copied_genome]
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477 self.subprocess_check_call(cmd)
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478
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479 # FAI Index
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480 cmd = ["samtools", "faidx", copied_genome + ".gz"]
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481 self.subprocess_check_call(cmd)
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482
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483 self.subprocess_check_call(
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diff changeset
484 [
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
485 "jbrowse",
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diff changeset
486 "add-assembly",
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diff changeset
487 "--load",
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488 "inPlace",
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diff changeset
489 "--name",
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490 uniq_label,
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491 "--type",
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492 "bgzipFasta",
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diff changeset
493 "--target",
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494 os.path.join(self.outdir, "data"),
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495 "--skipCheck",
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496 rel_seq_path + ".fasta.gz",
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497 ]
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diff changeset
498 )
13
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499
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500 return uniq_label
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501
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502 def text_index(self):
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503 # Index tracks
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504 args = [
14
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505 "jbrowse",
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506 "text-index",
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diff changeset
507 "--target",
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diff changeset
508 os.path.join(self.outdir, "data"),
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509 "--assemblies",
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diff changeset
510 self.current_assembly_id,
13
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511 ]
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512
14
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513 tracks = ",".join(self.tracksToIndex)
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514 if tracks:
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515 args += ["--tracks", tracks]
13
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516
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517 self.subprocess_check_call(args)
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diff changeset
518
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519 def _blastxml_to_gff3(self, xml, min_gap=10):
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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520 gff3_unrebased = tempfile.NamedTemporaryFile(delete=False)
14
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521 cmd = [
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diff changeset
522 "python",
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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523 os.path.join(INSTALLED_TO, "blastxml_to_gapped_gff3.py"),
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
524 "--trim",
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diff changeset
525 "--trim_end",
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
526 "--include_seq",
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diff changeset
527 "--min_gap",
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
528 str(min_gap),
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
529 xml,
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
530 ]
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
531 log.debug("cd %s && %s > %s", self.outdir, " ".join(cmd), gff3_unrebased.name)
13
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532 subprocess.check_call(cmd, cwd=self.outdir, stdout=gff3_unrebased)
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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533 gff3_unrebased.close()
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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534 return gff3_unrebased.name
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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535
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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536 def _prepare_track_style(self, xml_conf):
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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537
14
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538 style_data = {"type": "LinearBasicDisplay"}
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
539
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
540 if "display" in xml_conf["style"]:
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
541 style_data["type"] = xml_conf["style"]["display"]
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
542 del xml_conf["style"]["display"]
13
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543
14
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diff changeset
544 style_data["displayId"] = "%s_%s" % (xml_conf["label"], style_data["type"])
13
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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545
14
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diff changeset
546 style_data.update(xml_conf["style"])
13
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
547
14
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diff changeset
548 return {"displays": [style_data]}
13
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diff changeset
549
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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550 def add_blastxml(self, data, trackData, blastOpts, **kwargs):
14
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diff changeset
551 gff3 = self._blastxml_to_gff3(data, min_gap=blastOpts["min_gap"])
13
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552
14
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553 if "parent" in blastOpts and blastOpts["parent"] != "None":
13
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554 gff3_rebased = tempfile.NamedTemporaryFile(delete=False)
14
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
555 cmd = ["python", os.path.join(INSTALLED_TO, "gff3_rebase.py")]
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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556 if blastOpts.get("protein", "false") == "true":
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
557 cmd.append("--protein2dna")
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
558 cmd.extend([os.path.realpath(blastOpts["parent"]), gff3])
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
559 log.debug("cd %s && %s > %s", self.outdir, " ".join(cmd), gff3_rebased.name)
13
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
560 subprocess.check_call(cmd, cwd=self.outdir, stdout=gff3_rebased)
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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561 gff3_rebased.close()
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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562
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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563 # Replace original gff3 file
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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564 shutil.copy(gff3_rebased.name, gff3)
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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565 os.unlink(gff3_rebased.name)
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
566
14
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diff changeset
567 rel_dest = os.path.join("data", trackData["label"] + ".gff")
13
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
568 dest = os.path.join(self.outdir, rel_dest)
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
569
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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570 self._sort_gff(gff3, dest)
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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571 os.unlink(gff3)
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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572
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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573 style_json = self._prepare_track_style(trackData)
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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574
14
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
575 self._add_track(
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
576 trackData["label"],
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
577 trackData["key"],
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
578 trackData["category"],
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
579 rel_dest + ".gz",
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
580 config=style_json,
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
581 )
13
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diff changeset
582
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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583 def add_bigwig(self, data, trackData, wiggleOpts, **kwargs):
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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584
14
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
585 rel_dest = os.path.join("data", trackData["label"] + ".bw")
13
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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586 dest = os.path.join(self.outdir, rel_dest)
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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587 self.symlink_or_copy(os.path.realpath(data), dest)
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
588
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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589 style_json = self._prepare_track_style(trackData)
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
590
14
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591 self._add_track(
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
592 trackData["label"],
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
593 trackData["key"],
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
594 trackData["category"],
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
595 rel_dest,
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
596 config=style_json,
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
597 )
13
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diff changeset
598
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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599 # Anything ending in "am" (Bam or Cram)
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diff changeset
600 def add_xam(self, data, trackData, xamOpts, index=None, ext="bam", **kwargs):
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
601
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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602 index_ext = "bai"
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603 if ext == "cram":
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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604 index_ext = "crai"
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
605
14
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606 rel_dest = os.path.join("data", trackData["label"] + ".%s" % ext)
13
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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607 dest = os.path.join(self.outdir, rel_dest)
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608
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609 self.symlink_or_copy(os.path.realpath(data), dest)
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diff changeset
610
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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611 if index is not None and os.path.exists(os.path.realpath(index)):
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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612 # xai most probably made by galaxy and stored in galaxy dirs, need to copy it to dest
14
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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613 self.subprocess_check_call(
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diff changeset
614 ["cp", os.path.realpath(index), dest + ".%s" % index_ext]
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
615 )
13
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
616 else:
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617 # Can happen in exotic condition
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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618 # e.g. if bam imported as symlink with datatype=unsorted.bam, then datatype changed to bam
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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619 # => no index generated by galaxy, but there might be one next to the symlink target
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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620 # this trick allows to skip the bam sorting made by galaxy if already done outside
14
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diff changeset
621 if os.path.exists(os.path.realpath(data) + ".%s" % index_ext):
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
622 self.symlink_or_copy(
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
623 os.path.realpath(data) + ".%s" % index_ext, dest + ".%s" % index_ext
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
624 )
13
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
625 else:
14
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diff changeset
626 log.warn(
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
627 "Could not find a bam index (.%s file) for %s", (index_ext, data)
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
628 )
13
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
629
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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630 style_json = self._prepare_track_style(trackData)
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
631
14
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diff changeset
632 self._add_track(
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
633 trackData["label"],
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
634 trackData["key"],
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
635 trackData["category"],
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
636 rel_dest,
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
637 config=style_json,
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
638 )
13
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
639
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
640 def add_vcf(self, data, trackData, vcfOpts={}, zipped=False, **kwargs):
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
641
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
642 if zipped:
14
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
643 rel_dest = os.path.join("data", trackData["label"] + ".vcf.gz")
13
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
644 dest = os.path.join(self.outdir, rel_dest)
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
645 shutil.copy(os.path.realpath(data), dest)
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
646 else:
14
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diff changeset
647 rel_dest = os.path.join("data", trackData["label"] + ".vcf")
13
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
648 dest = os.path.join(self.outdir, rel_dest)
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
649 shutil.copy(os.path.realpath(data), dest)
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
650
14
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diff changeset
651 cmd = ["bgzip", dest]
13
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
652 self.subprocess_check_call(cmd)
14
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diff changeset
653 cmd = ["tabix", dest + ".gz"]
13
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
654 self.subprocess_check_call(cmd)
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
655
14
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diff changeset
656 rel_dest = os.path.join("data", trackData["label"] + ".vcf.gz")
13
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
657
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
658 style_json = self._prepare_track_style(trackData)
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
659
14
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
660 self._add_track(
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
661 trackData["label"],
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
662 trackData["key"],
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
663 trackData["category"],
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
664 rel_dest,
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
665 config=style_json,
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
666 )
13
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
667
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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668 def add_gff(self, data, format, trackData, gffOpts, **kwargs):
14
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
669 rel_dest = os.path.join("data", trackData["label"] + ".gff")
13
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
670 dest = os.path.join(self.outdir, rel_dest)
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
671
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
672 self._sort_gff(data, dest)
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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parents:
diff changeset
673
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
674 style_json = self._prepare_track_style(trackData)
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
675
14
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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parents: 13
diff changeset
676 self._add_track(
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
677 trackData["label"],
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
678 trackData["key"],
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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parents: 13
diff changeset
679 trackData["category"],
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
680 rel_dest + ".gz",
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
681 config=style_json,
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
682 )
13
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
683
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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684 def add_bed(self, data, format, trackData, gffOpts, **kwargs):
14
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
685 rel_dest = os.path.join("data", trackData["label"] + ".bed")
13
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
686 dest = os.path.join(self.outdir, rel_dest)
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
687
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diff changeset
688 self._sort_bed(data, dest)
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
689
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diff changeset
690 style_json = self._prepare_track_style(trackData)
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
691
14
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diff changeset
692 self._add_track(
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
693 trackData["label"],
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
694 trackData["key"],
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
695 trackData["category"],
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
696 rel_dest + ".gz",
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
697 config=style_json,
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
698 )
13
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diff changeset
699
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
700 def add_paf(self, data, trackData, pafOpts, **kwargs):
14
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
701 rel_dest = os.path.join("data", trackData["label"] + ".paf")
13
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diff changeset
702 dest = os.path.join(self.outdir, rel_dest)
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
703
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
704 self.symlink_or_copy(os.path.realpath(data), dest)
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
705
14
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diff changeset
706 added_assembly = self.add_assembly(
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
707 pafOpts["genome"], pafOpts["genome_label"], default=False
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
708 )
13
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
709
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
710 style_json = self._prepare_track_style(trackData)
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
711
14
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diff changeset
712 self._add_track(
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
713 trackData["label"],
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
714 trackData["key"],
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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parents: 13
diff changeset
715 trackData["category"],
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
716 rel_dest,
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
717 assemblies=[self.current_assembly_id, added_assembly],
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
718 config=style_json,
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
719 )
13
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
720
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
721 def add_hic(self, data, trackData, hicOpts, **kwargs):
14
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
722 rel_dest = os.path.join("data", trackData["label"] + ".hic")
13
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
723 dest = os.path.join(self.outdir, rel_dest)
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
724
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
725 self.symlink_or_copy(os.path.realpath(data), dest)
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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parents:
diff changeset
726
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
727 style_json = self._prepare_track_style(trackData)
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
728
14
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
729 self._add_track(
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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parents: 13
diff changeset
730 trackData["label"],
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
731 trackData["key"],
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
732 trackData["category"],
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
733 rel_dest,
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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parents: 13
diff changeset
734 config=style_json,
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
735 )
13
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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parents:
diff changeset
736
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
737 def add_sparql(self, url, query, query_refnames, trackData):
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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parents:
diff changeset
738
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
739 json_track_data = {
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
740 "type": "FeatureTrack",
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
741 "trackId": id,
14
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
742 "name": trackData["label"],
13
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
743 "adapter": {
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
744 "type": "SPARQLAdapter",
14
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
745 "endpoint": {"uri": url, "locationType": "UriLocation"},
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
746 "queryTemplate": query,
13
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
747 },
14
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
748 "category": [trackData["category"]],
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
749 "assemblyNames": [self.current_assembly_id],
13
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
750 }
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
751
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
752 if query_refnames:
14
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
753 json_track_data["adapter"]["refNamesQueryTemplate"]: query_refnames
13
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
754
14
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
755 self.subprocess_check_call(
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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parents: 13
diff changeset
756 [
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
757 "jbrowse",
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
758 "add-track-json",
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
759 "--target",
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
760 os.path.join(self.outdir, "data"),
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
761 json_track_data,
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
762 ]
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
763 )
13
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
764
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
765 # Doesn't work as of 1.6.4, might work in the future
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
766 # self.subprocess_check_call([
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
767 # 'jbrowse', 'add-track',
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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768 # '--trackType', 'sparql',
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
769 # '--name', trackData['label'],
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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770 # '--category', trackData['category'],
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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771 # '--target', os.path.join(self.outdir, 'data'),
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
772 # '--trackId', id,
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
773 # '--config', '{"queryTemplate": "%s"}' % query,
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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parents:
diff changeset
774 # url])
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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parents:
diff changeset
775
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
776 def _add_track(self, id, label, category, path, assemblies=[], config=None):
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
fubar
parents:
diff changeset
777
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
778 assemblies_opt = self.current_assembly_id
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
779 if assemblies:
14
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
780 assemblies_opt = ",".join(assemblies)
13
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
fubar
parents:
diff changeset
781
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
fubar
parents:
diff changeset
782 cmd = [
14
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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parents: 13
diff changeset
783 "jbrowse",
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
784 "add-track",
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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parents: 13
diff changeset
785 "--load",
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
786 "inPlace",
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
787 "--name",
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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parents: 13
diff changeset
788 label,
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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parents: 13
diff changeset
789 "--category",
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
790 category,
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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parents: 13
diff changeset
791 "--target",
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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parents: 13
diff changeset
792 os.path.join(self.outdir, "data"),
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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parents: 13
diff changeset
793 "--trackId",
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
794 id,
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
795 "--assemblyNames",
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
796 assemblies_opt,
13
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
fubar
parents:
diff changeset
797 ]
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
fubar
parents:
diff changeset
798
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
fubar
parents:
diff changeset
799 if config:
14
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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parents: 13
diff changeset
800 cmd.append("--config")
13
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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parents:
diff changeset
801 cmd.append(json.dumps(config))
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
fubar
parents:
diff changeset
802
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
fubar
parents:
diff changeset
803 cmd.append(path)
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
fubar
parents:
diff changeset
804
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
fubar
parents:
diff changeset
805 self.subprocess_check_call(cmd)
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
fubar
parents:
diff changeset
806
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
fubar
parents:
diff changeset
807 def _sort_gff(self, data, dest):
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
fubar
parents:
diff changeset
808 # Only index if not already done
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
fubar
parents:
diff changeset
809 if not os.path.exists(dest):
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
fubar
parents:
diff changeset
810 cmd = "gff3sort.pl --precise '%s' | grep -v \"^$\" > '%s'" % (data, dest)
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
fubar
parents:
diff changeset
811 self.subprocess_popen(cmd)
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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parents:
diff changeset
812
14
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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parents: 13
diff changeset
813 self.subprocess_check_call(["bgzip", "-f", dest])
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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parents: 13
diff changeset
814 self.subprocess_check_call(["tabix", "-f", "-p", "gff", dest + ".gz"])
13
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
fubar
parents:
diff changeset
815
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
fubar
parents:
diff changeset
816 def _sort_bed(self, data, dest):
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
fubar
parents:
diff changeset
817 # Only index if not already done
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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parents:
diff changeset
818 if not os.path.exists(dest):
14
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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parents: 13
diff changeset
819 cmd = ["sort", "-k1,1", "-k2,2n", data]
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
820 with open(dest, "w") as handle:
13
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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parents:
diff changeset
821 self.subprocess_check_call(cmd, output=handle)
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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parents:
diff changeset
822
14
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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parents: 13
diff changeset
823 self.subprocess_check_call(["bgzip", "-f", dest])
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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parents: 13
diff changeset
824 self.subprocess_check_call(["tabix", "-f", "-p", "bed", dest + ".gz"])
13
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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parents:
diff changeset
825
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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parents:
diff changeset
826 def process_annotations(self, track):
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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parents:
diff changeset
827
14
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
828 category = track["category"].replace("__pd__date__pd__", TODAY)
13
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
829 outputTrackConfig = {
14
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
830 "category": category,
13
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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parents:
diff changeset
831 }
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
832
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
833 mapped_chars = {
14
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
834 ">": "__gt__",
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
835 "<": "__lt__",
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
836 "'": "__sq__",
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
837 '"': "__dq__",
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
838 "[": "__ob__",
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
839 "]": "__cb__",
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
840 "{": "__oc__",
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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parents: 13
diff changeset
841 "}": "__cc__",
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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parents: 13
diff changeset
842 "@": "__at__",
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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parents: 13
diff changeset
843 "#": "__pd__",
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
844 "": "__cn__",
13
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
fubar
parents:
diff changeset
845 }
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
846
14
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
847 for i, (
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
848 dataset_path,
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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parents: 13
diff changeset
849 dataset_ext,
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
850 track_human_label,
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
851 extra_metadata,
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
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diff changeset
852 ) in enumerate(track["trackfiles"]):
13
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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parents:
diff changeset
853 # Unsanitize labels (element_identifiers are always sanitized by Galaxy)
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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parents:
diff changeset
854 for key, value in mapped_chars.items():
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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parents:
diff changeset
855 track_human_label = track_human_label.replace(value, key)
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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parents:
diff changeset
856
14
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
857 log.info(
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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parents: 13
diff changeset
858 "Processing track %s / %s (%s)",
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
859 category,
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
860 track_human_label,
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
861 dataset_ext,
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
862 )
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
863 outputTrackConfig["key"] = track_human_label
13
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
fubar
parents:
diff changeset
864 # We add extra data to hash for the case of REST + SPARQL.
14
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
865 if (
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
866 "conf" in track
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
867 and "options" in track["conf"]
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
868 and "url" in track["conf"]["options"]
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
869 ):
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
870 rest_url = track["conf"]["options"]["url"]
13
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
fubar
parents:
diff changeset
871 else:
14
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
872 rest_url = ""
13
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
fubar
parents:
diff changeset
873
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
fubar
parents:
diff changeset
874 # I chose to use track['category'] instead of 'category' here. This
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
fubar
parents:
diff changeset
875 # is intentional. This way re-running the tool on a different date
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
fubar
parents:
diff changeset
876 # will not generate different hashes and make comparison of outputs
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
fubar
parents:
diff changeset
877 # much simpler.
14
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
878 hashData = [
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
879 str(dataset_path),
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
880 track_human_label,
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
881 track["category"],
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
882 rest_url,
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
883 self.current_assembly_id,
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
884 ]
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
885 hashData = "|".join(hashData).encode("utf-8")
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
886 outputTrackConfig["label"] = hashlib.md5(hashData).hexdigest() + "_%s" % i
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
887 outputTrackConfig["metadata"] = extra_metadata
13
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
fubar
parents:
diff changeset
888
14
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
889 outputTrackConfig["style"] = track["style"]
13
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
fubar
parents:
diff changeset
890
14
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
891 if "menus" in track["conf"]["options"]:
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
892 menus = self.cs.parse_menus(track["conf"]["options"])
13
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
fubar
parents:
diff changeset
893 outputTrackConfig.update(menus)
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
fubar
parents:
diff changeset
894
14
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
895 if dataset_ext in ("gff", "gff3"):
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
896 self.add_gff(
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
897 dataset_path,
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
898 dataset_ext,
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
899 outputTrackConfig,
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
900 track["conf"]["options"]["gff"],
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
901 )
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
902 elif dataset_ext == "bed":
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
903 self.add_bed(
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
904 dataset_path,
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
905 dataset_ext,
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
906 outputTrackConfig,
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
907 track["conf"]["options"]["gff"],
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
908 )
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
909 elif dataset_ext == "bigwig":
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
910 self.add_bigwig(
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
911 dataset_path, outputTrackConfig, track["conf"]["options"]["wiggle"]
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
912 )
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
913 elif dataset_ext == "bam":
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
914 real_indexes = track["conf"]["options"]["pileup"]["bam_indices"][
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
915 "bam_index"
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
916 ]
13
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
fubar
parents:
diff changeset
917 if not isinstance(real_indexes, list):
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
fubar
parents:
diff changeset
918 # <bam_indices>
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
fubar
parents:
diff changeset
919 # <bam_index>/path/to/a.bam.bai</bam_index>
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
fubar
parents:
diff changeset
920 # </bam_indices>
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
fubar
parents:
diff changeset
921 #
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
fubar
parents:
diff changeset
922 # The above will result in the 'bam_index' key containing a
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
fubar
parents:
diff changeset
923 # string. If there are two or more indices, the container
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
fubar
parents:
diff changeset
924 # becomes a list. Fun!
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
fubar
parents:
diff changeset
925 real_indexes = [real_indexes]
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
fubar
parents:
diff changeset
926
14
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
927 self.add_xam(
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
928 dataset_path,
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
929 outputTrackConfig,
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
930 track["conf"]["options"]["pileup"],
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
931 index=real_indexes[i],
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
932 ext="bam",
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
933 )
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
934 elif dataset_ext == "cram":
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
935 real_indexes = track["conf"]["options"]["cram"]["cram_indices"][
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
936 "cram_index"
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
937 ]
13
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
fubar
parents:
diff changeset
938 if not isinstance(real_indexes, list):
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
fubar
parents:
diff changeset
939 # <bam_indices>
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
fubar
parents:
diff changeset
940 # <bam_index>/path/to/a.bam.bai</bam_index>
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
fubar
parents:
diff changeset
941 # </bam_indices>
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
fubar
parents:
diff changeset
942 #
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
fubar
parents:
diff changeset
943 # The above will result in the 'bam_index' key containing a
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
fubar
parents:
diff changeset
944 # string. If there are two or more indices, the container
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
fubar
parents:
diff changeset
945 # becomes a list. Fun!
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
fubar
parents:
diff changeset
946 real_indexes = [real_indexes]
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
947
14
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diff changeset
948 self.add_xam(
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
949 dataset_path,
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
950 outputTrackConfig,
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
951 track["conf"]["options"]["cram"],
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
952 index=real_indexes[i],
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
953 ext="cram",
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
954 )
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
955 elif dataset_ext == "blastxml":
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
956 self.add_blastxml(
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
957 dataset_path, outputTrackConfig, track["conf"]["options"]["blast"]
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
958 )
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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959 elif dataset_ext == "vcf":
13
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960 self.add_vcf(dataset_path, outputTrackConfig)
14
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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961 elif dataset_ext == "vcf_bgzip":
13
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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962 self.add_vcf(dataset_path, outputTrackConfig, zipped=True)
14
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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963 elif dataset_ext == "rest":
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
964 self.add_rest(
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
965 track["conf"]["options"]["rest"]["url"], outputTrackConfig
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
966 )
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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967 elif dataset_ext == "synteny":
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
968 self.add_paf(
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
969 dataset_path, outputTrackConfig, track["conf"]["options"]["synteny"]
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
970 )
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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971 elif dataset_ext == "hic":
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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972 self.add_hic(
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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973 dataset_path, outputTrackConfig, track["conf"]["options"]["hic"]
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
974 )
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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975 elif dataset_ext == "sparql":
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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976 sparql_query = track["conf"]["options"]["sparql"]["query"]
13
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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977 for key, value in mapped_chars.items():
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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978 sparql_query = sparql_query.replace(value, key)
14
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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979 sparql_query_refnames = track["conf"]["options"]["sparql"][
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
980 "query_refnames"
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
981 ]
13
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982 for key, value in mapped_chars.items():
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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983 sparql_query_refnames = sparql_query_refnames.replace(value, key)
14
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
984 self.add_sparql(
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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985 track["conf"]["options"]["sparql"]["url"],
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
986 sparql_query,
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
987 sparql_query_refnames,
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
988 outputTrackConfig,
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
989 )
13
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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990 else:
14
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991 log.warn("Do not know how to handle %s", dataset_ext)
13
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992
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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993 # Return non-human label for use in other fields
14
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
994 yield outputTrackConfig["label"]
13
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diff changeset
995
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996 def add_default_session(self, data):
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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997 """
14
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diff changeset
998 Add some default session settings: set some assemblies/tracks on/off
13
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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999 """
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
1000 tracks_data = []
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
1001
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
1002 # TODO using the default session for now, but check out session specs in the future https://github.com/GMOD/jbrowse-components/issues/2708
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
1003
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1004 # We need to know the track type from the config.json generated just before
14
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diff changeset
1005 config_path = os.path.join(self.outdir, "data", "config.json")
13
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1006 track_types = {}
14
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1007 with open(config_path, "r") as config_file:
13
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1008 config_json = json.load(config_file)
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1009
14
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1010 for track_conf in config_json["tracks"]:
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1011 track_types[track_conf["trackId"]] = track_conf["type"]
13
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1012
14
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1013 for on_track in data["visibility"]["default_on"]:
13
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1014 # TODO several problems with this currently
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1015 # - we are forced to copy the same kind of style config as the per track config from _prepare_track_style (not exactly the same though)
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1016 # - we get an error when refreshing the page
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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1017 # - this could be solved by session specs, see https://github.com/GMOD/jbrowse-components/issues/2708
14
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1018 style_data = {"type": "LinearBasicDisplay", "height": 100}
13
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diff changeset
1019
14
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1020 if on_track in data["style"]:
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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1021 if "display" in data["style"][on_track]:
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1022 style_data["type"] = data["style"][on_track]["display"]
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diff changeset
1023 del data["style"][on_track]["display"]
13
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1024
14
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diff changeset
1025 style_data.update(data["style"][on_track])
13
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1026
14
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diff changeset
1027 if on_track in data["style_labels"]:
13
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diff changeset
1028 # TODO fix this: it should probably go in a renderer block (SvgFeatureRenderer) but still does not work
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1029 # TODO move this to per track displays?
14
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1030 style_data["labels"] = data["style_labels"][on_track]
13
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diff changeset
1031
14
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diff changeset
1032 tracks_data.append(
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diff changeset
1033 {
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
1034 "type": track_types[on_track],
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
1035 "configuration": on_track,
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
1036 "displays": [style_data],
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
1037 }
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
1038 )
13
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diff changeset
1039
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diff changeset
1040 # The view for the assembly we're adding
14
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diff changeset
1041 view_json = {"type": "LinearGenomeView", "tracks": tracks_data}
13
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diff changeset
1042
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diff changeset
1043 refName = None
14
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diff changeset
1044 if data.get("defaultLocation", ""):
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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1045 loc_match = re.search(r"^(\w+):(\d+)\.+(\d+)$", data["defaultLocation"])
13
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diff changeset
1046 if loc_match:
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
1047 refName = loc_match.group(1)
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
1048 start = int(loc_match.group(2))
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
1049 end = int(loc_match.group(3))
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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1050 elif self.assembly_ids[self.current_assembly_id] is not None:
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diff changeset
1051 refName = self.assembly_ids[self.current_assembly_id]
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diff changeset
1052 start = 0
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
1053 end = 1000000 # Booh, hard coded! waiting for https://github.com/GMOD/jbrowse-components/issues/2708
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diff changeset
1054
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1055 if refName is not None:
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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1056 # TODO displayedRegions is not just zooming to the region, it hides the rest of the chromosome
14
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1057 view_json["displayedRegions"] = [
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
1058 {
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diff changeset
1059 "refName": refName,
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diff changeset
1060 "start": start,
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diff changeset
1061 "end": end,
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
1062 "reversed": False,
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
1063 "assemblyName": self.current_assembly_id,
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
1064 }
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
1065 ]
13
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1066
14
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1067 session_name = data.get("session_name", "New session")
13
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1068 if not session_name:
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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1069 session_name = "New session"
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diff changeset
1070
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1071 # Merge with possibly existing defaultSession (if upgrading a jbrowse instance)
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1072 session_json = {}
14
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diff changeset
1073 if "defaultSession" in config_json:
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
1074 session_json = config_json["defaultSession"]
13
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diff changeset
1075
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1076 session_json["name"] = session_name
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diff changeset
1077
14
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1078 if "views" not in session_json:
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diff changeset
1079 session_json["views"] = []
13
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1080
14
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diff changeset
1081 session_json["views"].append(view_json)
13
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diff changeset
1082
14
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diff changeset
1083 config_json["defaultSession"] = session_json
13
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diff changeset
1084
14
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diff changeset
1085 with open(config_path, "w") as config_file:
13
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1086 json.dump(config_json, config_file, indent=2)
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1087
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1088 def add_general_configuration(self, data):
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1089 """
14
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diff changeset
1090 Add some general configuration to the config.json file
13
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1091 """
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1092
14
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1093 config_path = os.path.join(self.outdir, "data", "config.json")
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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1094 with open(config_path, "r") as config_file:
13
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1095 config_json = json.load(config_file)
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1096
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1097 config_data = {}
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1098
14
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1099 config_data["disableAnalytics"] = data.get("analytics", "false") == "true"
13
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1100
14
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1101 config_data["theme"] = {
13
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1102 "palette": {
14
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1103 "primary": {"main": data.get("primary_color", "#0D233F")},
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1104 "secondary": {"main": data.get("secondary_color", "#721E63")},
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1105 "tertiary": {"main": data.get("tertiary_color", "#135560")},
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1106 "quaternary": {"main": data.get("quaternary_color", "#FFB11D")},
13
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1107 },
14
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1108 "typography": {"fontSize": int(data.get("font_size", 10))},
13
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1109 }
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diff changeset
1110
14
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1111 config_json["configuration"].update(config_data)
13
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1112
14
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diff changeset
1113 with open(config_path, "w") as config_file:
13
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1114 json.dump(config_json, config_file, indent=2)
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diff changeset
1115
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
1116 def clone_jbrowse(self, jbrowse_dir, destination):
14
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
1117 """Clone a JBrowse directory into a destination directory."""
13
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
1118
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
1119 copytree(jbrowse_dir, destination)
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
1120
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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parents:
diff changeset
1121 try:
14
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
1122 shutil.rmtree(os.path.join(destination, "test_data"))
13
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
1123 except OSError as e:
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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parents:
diff changeset
1124 log.error("Error: %s - %s." % (e.filename, e.strerror))
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
1125
14
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
1126 if not os.path.exists(os.path.join(destination, "data")):
13
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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parents:
diff changeset
1127 # It can already exist if upgrading an instance
14
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
1128 os.makedirs(os.path.join(destination, "data"))
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
1129 log.info("makedir %s" % (os.path.join(destination, "data")))
13
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
1130
14
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
1131 os.symlink("./data/config.json", os.path.join(destination, "config.json"))
13
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
1132
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
1133
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
1134 def copytree(src, dst, symlinks=False, ignore=None):
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
1135 for item in os.listdir(src):
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
1136 s = os.path.join(src, item)
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
1137 d = os.path.join(dst, item)
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
1138 if os.path.isdir(s):
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
1139 shutil.copytree(s, d, symlinks, ignore)
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
1140 else:
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
1141 shutil.copy2(s, d)
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
1142
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
1143
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
1144 def parse_style_conf(item):
14
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
1145 if "type" in item.attrib and item.attrib["type"] in ["boolean", "integer"]:
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
1146 if item.attrib["type"] == "boolean":
13
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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parents:
diff changeset
1147 return item.text in ("yes", "true", "True")
14
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
1148 elif item.attrib["type"] == "integer":
13
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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parents:
diff changeset
1149 return int(item.text)
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
1150 else:
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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parents:
diff changeset
1151 return item.text
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
1152
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
1153
14
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
1154 if __name__ == "__main__":
13
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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parents:
diff changeset
1155 parser = argparse.ArgumentParser(description="", epilog="")
14
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
1156 parser.add_argument("xml", type=argparse.FileType("r"), help="Track Configuration")
13
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
1157
14
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
1158 parser.add_argument("--jbrowse", help="Folder containing a jbrowse release")
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
1159 parser.add_argument("--outdir", help="Output directory", default="out")
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
1160 parser.add_argument("--version", "-V", action="version", version="%(prog)s 0.8.0")
13
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diff changeset
1161 args = parser.parse_args()
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
1162
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
1163 tree = ET.parse(args.xml.name)
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
1164 root = tree.getroot()
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
1165
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
1166 # This should be done ASAP
14
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
1167 GALAXY_INFRASTRUCTURE_URL = root.find("metadata/galaxyUrl").text
13
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
1168 # Sometimes this comes as `localhost` without a protocol
14
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diff changeset
1169 if not GALAXY_INFRASTRUCTURE_URL.startswith("http"):
13
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
1170 # so we'll prepend `http://` and hope for the best. Requests *should*
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
1171 # be GET and not POST so it should redirect OK
14
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diff changeset
1172 GALAXY_INFRASTRUCTURE_URL = "http://" + GALAXY_INFRASTRUCTURE_URL
13
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
1173
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
1174 jc = JbrowseConnector(
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
1175 jbrowse=args.jbrowse,
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
1176 outdir=args.outdir,
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
1177 genomes=[
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
1178 {
14
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
1179 "path": os.path.realpath(x.attrib["path"]),
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
1180 "meta": metadata_from_node(x.find("metadata")),
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
1181 "label": x.attrib["label"],
13
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
1182 }
14
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
1183 for x in root.findall("metadata/genomes/genome")
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
1184 ],
13
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
1185 )
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
1186
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
1187 default_session_data = {
14
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diff changeset
1188 "visibility": {
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
1189 "default_on": [],
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
1190 "default_off": [],
13
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diff changeset
1191 },
14
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
1192 "style": {},
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
1193 "style_labels": {},
13
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diff changeset
1194 }
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
1195
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
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diff changeset
1196 # TODO add metadata to tracks
14
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diff changeset
1197 for track in root.findall("tracks/track"):
13
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diff changeset
1198 track_conf = {}
14
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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diff changeset
1199 track_conf["trackfiles"] = []
13
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
fubar
parents:
diff changeset
1200
14
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
1201 trackfiles = track.findall("files/trackFile")
13
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
fubar
parents:
diff changeset
1202 if trackfiles:
14
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
1203 for x in track.findall("files/trackFile"):
13
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
fubar
parents:
diff changeset
1204 if trackfiles:
14
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
1205 metadata = metadata_from_node(x.find("metadata"))
13
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
fubar
parents:
diff changeset
1206
14
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
1207 track_conf["trackfiles"].append(
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
1208 (
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
1209 os.path.realpath(x.attrib["path"]),
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
1210 x.attrib["ext"],
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
1211 x.attrib["label"],
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
1212 metadata,
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
1213 )
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
1214 )
13
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
fubar
parents:
diff changeset
1215 else:
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
fubar
parents:
diff changeset
1216 # For tracks without files (rest, sparql)
14
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
1217 track_conf["trackfiles"].append(
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
1218 (
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
1219 "", # N/A, no path for rest or sparql
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
1220 track.attrib["format"],
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
1221 track.find("options/label").text,
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
1222 {},
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
1223 )
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
1224 )
13
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
fubar
parents:
diff changeset
1225
14
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
1226 track_conf["category"] = track.attrib["cat"]
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
1227 track_conf["format"] = track.attrib["format"]
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
1228 track_conf["style"] = {
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
1229 item.tag: parse_style_conf(item) for item in track.find("options/style")
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
1230 }
13
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
fubar
parents:
diff changeset
1231
14
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
1232 track_conf["style"] = {
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
1233 item.tag: parse_style_conf(item) for item in track.find("options/style")
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
1234 }
13
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
fubar
parents:
diff changeset
1235
14
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
1236 track_conf["style_labels"] = {
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
1237 item.tag: parse_style_conf(item)
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
1238 for item in track.find("options/style_labels")
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
1239 }
13
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
fubar
parents:
diff changeset
1240
14
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
1241 track_conf["conf"] = etree_to_dict(track.find("options"))
13
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
fubar
parents:
diff changeset
1242 keys = jc.process_annotations(track_conf)
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
fubar
parents:
diff changeset
1243
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
fubar
parents:
diff changeset
1244 for key in keys:
14
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
1245 default_session_data["visibility"][
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
1246 track.attrib.get("visibility", "default_off")
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
1247 ].append(key)
13
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
fubar
parents:
diff changeset
1248
14
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
1249 default_session_data["style"][key] = track_conf[
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
1250 "style"
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
1251 ] # TODO do we need this anymore?
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
1252 default_session_data["style_labels"][key] = track_conf["style_labels"]
13
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
fubar
parents:
diff changeset
1253
14
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
1254 default_session_data["defaultLocation"] = root.find(
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
1255 "metadata/general/defaultLocation"
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
1256 ).text
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
1257 default_session_data["session_name"] = root.find(
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
1258 "metadata/general/session_name"
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
1259 ).text
13
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
fubar
parents:
diff changeset
1260
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
fubar
parents:
diff changeset
1261 general_data = {
14
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
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parents: 13
diff changeset
1262 "analytics": root.find("metadata/general/analytics").text,
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
1263 "primary_color": root.find("metadata/general/primary_color").text,
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
1264 "secondary_color": root.find("metadata/general/secondary_color").text,
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
1265 "tertiary_color": root.find("metadata/general/tertiary_color").text,
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
1266 "quaternary_color": root.find("metadata/general/quaternary_color").text,
7c2e28e144f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
fubar
parents: 13
diff changeset
1267 "font_size": root.find("metadata/general/font_size").text,
13
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
fubar
parents:
diff changeset
1268 }
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
fubar
parents:
diff changeset
1269
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
fubar
parents:
diff changeset
1270 jc.add_default_session(default_session_data)
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
fubar
parents:
diff changeset
1271 jc.add_general_configuration(general_data)
1d86925dbb4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
fubar
parents:
diff changeset
1272 jc.text_index()