Mercurial > repos > iuc > jbrowse

annotate jbrowse.py @ 1:497c6bb3b717 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
author iuc
date Thu, 18 Jun 2015 12:10:51 -0400
parents 2c9e5136b416
children 7342f467507b
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2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
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diff changeset
1 #!/usr/bin/env python
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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2 from string import Template
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2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
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3 import os
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
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4 import argparse
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
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5 import subprocess
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
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6 import hashlib
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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7 import tempfile
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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8 import json
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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9 import yaml
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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10 import logging
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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11 logging.basicConfig()
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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12 log = logging.getLogger(__name__)
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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13
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14 COLOR_FUNCTION_TEMPLATE = Template("""
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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15 function(feature, variableName, glyphObject, track) {
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16 var score = ${score};
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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17 ${opacity}
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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18 return 'rgba(${red}, ${green}, ${blue}, ' + opacity + ')';
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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19 }
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20 """)
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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21
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22 BLAST_OPACITY_MATH = """
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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23 var opacity = 0;
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24 if(score == 0.0) {
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25 opacity = 1;
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26 } else{
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27 opacity = (20 - Math.log10(score)) / 180;
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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28 }
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29 """
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30
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31 BREWER_COLOUR_IDX = 0
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32 BREWER_COLOUR_SCHEMES = [
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33 (228, 26, 28),
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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34 (55, 126, 184),
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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35 (77, 175, 74),
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36 (152, 78, 163),
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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37 (255, 127, 0),
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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38 ]
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39
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40
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41 # score comes from feature._parent.get('score') or feature.get('score')
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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42 # Opacity math
0
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44 TN_TABLE = {
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45 'gff3': '--gff',
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46 'gff': '--gff',
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
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47 'bed': '--bed',
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48 # 'genbank': '--gbk',
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49 }
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50
1
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51 INSTALLED_TO = os.path.dirname(os.path.realpath(__file__))
0
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52
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53
1
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54 class JbrowseConnector(object):
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55
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56 def __init__(self, jbrowse, jbrowse_dir, outdir, genome):
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57 self.jbrowse = jbrowse
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58 self.jbrowse_dir = jbrowse_dir
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59 self.outdir = outdir
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60 self.genome_path = genome
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61 self.brewer_colour_idx = 0
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62
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63 self.clone_jbrowse(self.jbrowse, self.outdir)
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64 self.process_genome()
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65
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66 def subprocess_check_call(self, command):
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67 log.debug('cd %s && %s', self.jbrowse_dir, ' '.join(command))
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68 subprocess.check_call(command, cwd=self.jbrowse_dir)
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69
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70 def _get_colours(self):
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71 r, g, b = BREWER_COLOUR_SCHEMES[self.brewer_colour_idx]
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72 self.brewer_colour_idx += 1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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73 return r, g, b
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74
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75 def process_genome(self):
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76 self.subprocess_check_call(['perl', 'bin/prepare-refseqs.pl',
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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77 '--fasta', self.genome_path])
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78
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79 def _add_json(self, json_data):
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80 if len(json_data.keys()) == 0:
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81 return
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82
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83 tmp = tempfile.NamedTemporaryFile(delete=False)
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84 tmp.write(json.dumps(json_data))
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85 tmp.close()
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86 cmd = ['perl', 'bin/add-track-json.pl', tmp.name,
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87 os.path.join('data', 'trackList.json')]
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88 self.subprocess_check_call(cmd)
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89 os.unlink(tmp.name)
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90
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91 def add_blastxml(self, data, key, **kwargs):
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92 gff3_unrebased = tempfile.NamedTemporaryFile(delete=False)
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93 cmd = ['python', os.path.join(INSTALLED_TO, 'blastxml_to_gapped_gff3.py'),
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94 '--trim_end', '--min_gap', str(kwargs['min_gap']), data]
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95 subprocess.check_call(cmd, cwd=self.jbrowse_dir, stdout=gff3_unrebased)
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96 gff3_unrebased.close()
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97
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98 gff3_rebased = tempfile.NamedTemporaryFile(delete=False)
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99 cmd = ['python', os.path.join(INSTALLED_TO, 'gff3_rebase.py')]
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100 if kwargs['protein']:
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101 cmd.append('--protein2dna')
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102 cmd.extend([kwargs['parent'], gff3_unrebased.name])
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103 subprocess.check_call(cmd, cwd=self.jbrowse_dir, stdout=gff3_rebased)
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104 gff3_rebased.close()
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105
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106 label = hashlib.md5(data).hexdigest()
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107
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108 red, green, blue = self._get_colours()
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109 color_function = COLOR_FUNCTION_TEMPLATE.substitute({
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110 'score': "feature._parent.get('score')",
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111 'opacity': BLAST_OPACITY_MATH,
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112 'red': red,
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113 'green': green,
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114 'blue': blue,
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115 })
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116
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117 clientConfig = {
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118 'label': 'description',
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119 'color': color_function.replace('\n', ''),
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120 'description': 'Hit_titles',
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121 }
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122 config = {'glyph': 'JBrowse/View/FeatureGlyph/Segments'}
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123 if 'category' in kwargs:
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124 config['category'] = kwargs['category']
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125
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126 cmd = ['perl', 'bin/flatfile-to-json.pl',
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127 '--gff', gff3_rebased.name,
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128 '--trackLabel', label,
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129 '--key', key,
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130 '--clientConfig', json.dumps(clientConfig),
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131 '--config', json.dumps(config),
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132 '--trackType', 'JBrowse/View/Track/CanvasFeatures'
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133 ]
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134
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135 self.subprocess_check_call(cmd)
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136 os.unlink(gff3_rebased.name)
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137 os.unlink(gff3_unrebased.name)
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138
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139 def _min_max_gff(self, gff_file):
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140 min_val = None
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141 max_val = None
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142 with open(gff_file, 'r') as handle:
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143 for line in handle:
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144 try:
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145 value = float(line.split('\t')[5])
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146 min_val = min(value, (min_val or value))
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147 max_val = max(value, (max_val or value))
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148
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149 if value < min_val:
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150 min_val = value
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151
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152 if value > max_val:
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153 max_val = value
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154 except Exception:
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155 pass
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156 return min_val, max_val
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157
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158 def add_bigwig(self, data, key, **kwargs):
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159 label = hashlib.md5(data).hexdigest()
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160 dest = os.path.join('data', 'raw', os.path.basename(data))
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161 cmd = ['ln', '-s', data, dest]
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162 self.subprocess_check_call(cmd)
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163
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164 track_data = {
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165 "label": label,
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166 "urlTemplate": os.path.join('..', dest),
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167 "bicolor_pivot": "zero",
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168 "storeClass": "JBrowse/Store/SeqFeature/BigWig",
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169 "type": "JBrowse/View/Track/Wiggle/Density",
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170 "key": key,
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171 }
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172 track_data.update(kwargs)
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173
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174 if 'min' not in track_data and 'max' not in track_data \
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175 and 'autoscale' not in track_data:
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176 track_data['autoscale'] = 'local'
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177
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178 self._add_json(track_data)
0
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179
1
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180 def add_bam(self, data, key, **kwargs):
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181 label = hashlib.md5(data).hexdigest()
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182 dest = os.path.join('data', 'raw', os.path.basename(data))
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183 # ln?
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184 cmd = ['ln', '-s', data, dest]
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185 self.subprocess_check_call(cmd)
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186
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187 bai_source = kwargs['bam_index']
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188 cmd = ['ln', '-s', bai_source, dest + '.bai']
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189 self.subprocess_check_call(cmd)
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190
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191 track_data = {
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192 "urlTemplate": os.path.join('..', dest),
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193 "key": key,
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194 "label": label,
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195 "type": "JBrowse/View/Track/Alignments2",
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196 "storeClass": "JBrowse/Store/SeqFeature/BAM",
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197 }
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198 if 'category' in kwargs:
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199 track_data['category'] = kwargs['category']
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200 self._add_json(track_data)
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201
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202 if kwargs.get('auto_snp', False):
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203 track_data = {
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204 "storeClass": "JBrowse/Store/SeqFeature/BAM",
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205 "urlTemplate": os.path.join('..', dest),
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206 "type": "JBrowse/View/Track/SNPCoverage",
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207 "key": key + " - SNPs/Coverage",
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208 "label": label + "_autosnp",
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209 }
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210 if 'category' in kwargs:
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211 track_data['category'] = kwargs['category']
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212 self._add_json(track_data)
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213
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214 def add_vcf(self, data, key, **kwargs):
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215 label = hashlib.md5(data).hexdigest()
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216 dest = os.path.join('data', 'raw', os.path.basename(data))
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217 # ln?
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218 cmd = ['ln', '-s', data, dest]
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219 self.subprocess_check_call(cmd)
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220 cmd = ['bgzip', dest]
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221 self.subprocess_check_call(cmd)
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222 cmd = ['tabix', '-p', 'vcf', dest + '.gz']
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223 self.subprocess_check_call(cmd)
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224
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225 track_data = {
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226 "key": key,
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227 "label": label,
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228 "urlTemplate": os.path.join('..', dest + '.gz'),
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229 "type": "JBrowse/View/Track/HTMLVariants",
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230 "storeClass": "JBrowse/Store/SeqFeature/VCFTabix",
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231 }
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232 track_data.update(kwargs)
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233 self._add_json(track_data)
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234
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235 def add_features(self, data, key, format, **kwargs):
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236 label = hashlib.md5(data).hexdigest()
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237 cmd = ['perl', 'bin/flatfile-to-json.pl',
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238 TN_TABLE.get(format, 'gff'), data,
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239 '--trackLabel', label,
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240 '--key', key]
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241
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242 config = {}
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243 if 'category' in kwargs:
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244 config['category'] = kwargs['category']
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245
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246 if kwargs.get('match', False):
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247 clientConfig = {
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248 'label': 'description',
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249 'description': 'Hit_titles',
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250 }
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251
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252 # Get min/max and build a scoring function since JBrowse doesn't
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253 min_val, max_val = self._min_max_gff(data)
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254
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255 if min_val is not None and max_val is not None:
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256 MIN_MAX_OPACITY_MATH = Template("""
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257 var opacity = (score - ${min}) * (1/(${max} - ${min}));
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258 """).substitute({
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259 'max': max_val,
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260 'min': min_val,
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261 })
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262
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263 red, green, blue = self._get_colours()
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264 color_function = COLOR_FUNCTION_TEMPLATE.substitute({
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265 'score': "feature.get('score')",
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266 'opacity': MIN_MAX_OPACITY_MATH,
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267 'red': red,
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268 'green': green,
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269 'blue': blue,
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270 })
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271
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272 clientConfig['color'] = color_function.replace('\n', '')
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273
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274 config['glyph'] = 'JBrowse/View/FeatureGlyph/Segments'
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275
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276 cmd += ['--clientConfig', json.dumps(clientConfig),
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277 '--trackType', 'JBrowse/View/Track/CanvasFeatures'
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278 ]
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279
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280 cmd.extend(['--config', json.dumps(config)])
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281
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282 self.subprocess_check_call(cmd)
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283
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284 def process_annotations(self, data, key, format, **kwargs):
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285 if format in ('gff', 'gff3', 'bed'):
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286 self.add_features(data, key, format, **kwargs)
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287 elif format == 'bigwig':
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288 self.add_bigwig(data, key, **kwargs)
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289 elif format == 'bam':
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290 self.add_bam(data, key, **kwargs)
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291 elif format == 'blastxml':
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292 self.add_blastxml(data, key, **kwargs)
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293 elif format == 'vcf':
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294 self.add_vcf(data, key, **kwargs)
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295
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296 def clone_jbrowse(self, jbrowse_dir, destination):
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297 # JBrowse seems to have included some bad symlinks, cp ignores bad symlinks
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298 # unlike copytree
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299 cmd = ['mkdir', '-p', destination]
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300 subprocess.check_call(cmd)
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301 cmd = ['cp', '-r', jbrowse_dir, destination]
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302 subprocess.check_call(cmd)
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303 cmd = ['mkdir', '-p', os.path.join(destination, 'JBrowse-1.11.6',
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304 'data', 'raw')]
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305 subprocess.check_call(cmd)
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306
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307 # http://unix.stackexchange.com/a/38691/22785
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308 # JBrowse releases come with some broken symlinks
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309 cmd = ['find', destination, '-type', 'l', '-xtype', 'l', '-exec', 'rm', "'{}'", '+']
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310 subprocess.check_call(cmd)
0
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311
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312
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313 if __name__ == '__main__':
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314 parser = argparse.ArgumentParser(description="", epilog="")
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315 parser.add_argument('genome', type=file, help='Input genome file')
1
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316 parser.add_argument('yaml', type=file, help='Track Configuration')
0
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317
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318 parser.add_argument('--jbrowse', help='Folder containing a jbrowse release')
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319 parser.add_argument('--outdir', help='Output directory', default='out')
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320 args = parser.parse_args()
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321
1
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322 jc = JbrowseConnector(
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323 jbrowse=args.jbrowse,
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324 jbrowse_dir=os.path.join(args.outdir, 'JBrowse-1.11.6'),
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325 outdir=args.outdir,
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326 genome=os.path.realpath(args.genome.name),
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327 )
0
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328
1
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329 track_data = yaml.load(args.yaml)
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330 for track in track_data:
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331 path = os.path.realpath(track['file'])
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332 extra = track.get('options', {})
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333 if '__unused__' in extra:
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334 del extra['__unused__']
0
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335
1
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336 for possible_partial_path in ('bam_index', 'parent'):
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337 if possible_partial_path in extra:
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338 extra[possible_partial_path] = os.path.realpath(
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339 extra[possible_partial_path])
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340 extra['category'] = track.get('category', 'Default')
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341
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342 jc.process_annotations(path, track['label'], track['ext'], **extra)
0
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343
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344 print """
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345 <html>
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346 <body>
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347 <script type="text/javascript">
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348 window.location=JBrowse-1.11.6/index.html
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349 </script>
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350 <a href="JBrowse-1.11.6/index.html">Go to JBrowse</a>
1
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351 <p>Please note that JBrowse functions best on production Galaxy
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352 instances. The paste server used in development instances has issues
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353 serving the volumes of data regularly involved in JBrowse</p>
0
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354 </body>
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355 </html>
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356 """