Mercurial > repos > fubar > jbrowse2

annotate autogenJB2.py @ 114:75f01bd05bd8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2f823945594c6e61a7661c253b671a604b8fb959
author bgruening
date Tue, 20 Aug 2024 06:43:01 +0000
parents 878c27dfea9d
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 import argparse
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2 import logging
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3 import os
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4 import sys
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5
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6 from jbrowse2 import JbrowseConnector as jbC
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7
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9 logging.basicConfig(level=logging.DEBUG)
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10 log = logging.getLogger("jbrowse")
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12 if __name__ == "__main__":
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13 parser = argparse.ArgumentParser(description="", epilog="")
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14 parser.add_argument("--sessName", help="Session name", default="AutoJBrowse")
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15 parser.add_argument(
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16 "--trackmeta",
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17 help="Repeatable 'filename,filext,filepath,[bai/crai path for filesystem bam/cram]' for JBrowse2 tracks",
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18 default=[],
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19 action="append",
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20 )
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21 parser.add_argument(
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22 "--referencemeta",
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23 help="Repeatable 'filename, filext, filepath, ... ,' for JBrowse2 reference tracks - usually only one needed",
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24 default=[],
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25 action="append",
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26 )
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27 parser.add_argument(
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28 "--pafmeta",
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29 help="Repeatable. Each is a 'pafname, filext, filepath, ... ,' for a JBrowse2 paf track",
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30 default=[],
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31 action="append",
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32 )
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33 parser.add_argument(
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34 "--pafreferencemeta",
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35 help="Repeatable. Each is a 'pafname,refpath,refname' Every pafname must have one or more",
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36 default=[],
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37 action="append",
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38 )
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39 parser.add_argument(
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40 "--jbrowse2path", help="Path to JBrowse2 directory in biocontainer or Conda"
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41 )
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42 parser.add_argument("--outdir", help="Output directory", required=True)
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43 parser.add_argument("--version", "-V", action="version", version="%(prog)s 2.10.2")
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44 args = parser.parse_args()
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45 sessName = args.sessName
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46 default_session_data = {}
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47 # --trackmeta $jbrowseme[$key],$jbrowseme[$key].ext,'$key'
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48 trackList = [x.strip().split(",") for x in args.trackmeta if x > ""]
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49 refList = [x.strip().split(",") for x in args.referencemeta if x > ""]
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50 if len(refList) > 0:
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51 listgenomes = [f for f in refList if f[1] in ["fasta", "fasta.gz"]]
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52 # assume no pafs here
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53 if len(listgenomes) > 0:
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54 genome_paths = [x[0] for x in listgenomes]
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55 genome_names = [x[2] for x in listgenomes]
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56 guseuri = []
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57 for x in genome_paths:
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58 if x.startswith("http://") or x.startswith("https://"):
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59 guseuri.append("yes")
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60 else:
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61 guseuri.append("no")
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62 jc = jbC(
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63 outdir=args.outdir,
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64 jbrowse2path=args.jbrowse2path,
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65 )
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66 genomes = (
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67 [
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68 {
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69 "path": x,
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70 "label": genome_names[i],
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71 "useuri": guseuri[i],
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72 "meta": {
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73 "name": genome_names[i],
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74 "dataset_dname": genome_names[i],
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75 },
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76 }
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77 for i, x in enumerate(genome_paths)
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78 ],
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79 )
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80 assref_name = jc.process_genomes(genomes[0])
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81 if not default_session_data.get(assref_name, None):
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82 default_session_data[assref_name] = {
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83 "tracks": [],
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84 "style": {},
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85 "style_labels": {},
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86 "visibility": {
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87 "default_on": [],
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88 "default_off": [],
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89 },
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90 }
35
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91 listtracks = trackList
98
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92 # foo.paf must have a foo_paf.fasta or fasta.gz to match
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93 tnames = [x[2] for x in listtracks]
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94 texts = [x[1] for x in listtracks]
113
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95 if len(listtracks) == 0:
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96 sys.stderr.write(
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97 "Please add at least one track (bam,bed,bigwig,blastxml,cram,gff,hic,maf,paf or vcf) to the collection. No suitable track files for autogenJB2 - nothing to process"
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98 )
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99 sys.exit(5)
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100 for i, track in enumerate(listtracks):
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101 track_conf = {
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102 "trackfiles": [],
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103 "category": "autogenerated",
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104 "assemblyNames": assref_name,
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105 }
35
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106 tpath, trext, trackname = track[:3]
48
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107 track_conf["dataset_id"] = trackname
52
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108 useuri = "no"
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109 if tpath.startswith("http://") or tpath.startswith("https://"):
52
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110 useuri = "yes"
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111 if trext == "paf":
98
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112 refname = trackname + "_paf.fasta"
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113 refdat = [x[2] for x in listtracks if x[2] == refname]
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114 if not refdat:
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115 jc.logging.warn(
98
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116 "No reference file %s corresponding to paf file %s found. Not building - there must be a corresponding fasta for each paf"
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117 % (refname, trackname)
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118 )
98
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119 sys.exit(3)
30
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120 else:
57
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121 track_conf.update(
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122 {
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123 "conf": {
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124 "options": {
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125 "paf": {
98
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126 "genome": refdat,
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127 "genome_label": trackname,
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128 }
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129 }
30
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130 }
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131 }
57
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132 )
46
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133 elif trext == "bam":
57
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134 ipath = track[3]
46
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135 if not os.path.exists(ipath):
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136 ipath = os.path.realpath(
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137 os.path.join(jc.outdir, trackname + ".bai")
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138 )
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139 cmd = [
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140 "samtools",
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141 "index",
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142 "-b",
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143 "-o",
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144 ipath,
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145 os.path.realpath(track[0]),
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146 ]
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147 sys.stdout.write("#### calling %s" % " ".join(cmd))
46
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148 jc.subprocess_check_call(cmd)
57
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149 track_conf.update(
98
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150 {"conf": {"options": {"bam": {"bam_index": " %s ~ %s," % (tpath, ipath)}}}}
57
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151 )
46
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152 elif trext == "cram":
57
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153 ipath = track[3]
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154 if not os.path.exists(ipath):
57
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155 ipath = os.path.realpath(
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156 os.path.join("./", trackname + ".crai")
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157 )
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158 cmd = [
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159 "samtools",
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160 "index",
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161 "-c",
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162 "-o",
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163 ipath,
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164 os.path.realpath(track[0]),
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165 ]
46
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166 jc.subprocess_check_call(cmd)
57
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167 track_conf.update(
93
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168 {"conf": {"options": {"cram": {"cram_index": "%s ~ %s," % (tpath, ipath)}}}}
57
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169 )
48
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170 track_conf["path"] = tpath
35
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171 track_conf["format"] = trext
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172 track_conf["name"] = trackname
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173 track_conf["label"] = trackname
52
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174 track_conf["trackfiles"].append((tpath, trext, useuri, trackname, {}))
30
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175 keys = jc.process_annotations(track_conf)
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176
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177 if keys:
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178 for key in keys:
46
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179 if trext in [
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180 "bigwig",
67
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181 "gff",
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182 "gff3",
46
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183 "vcf",
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184 "maf",
72
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185 "bed",
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186 "hic"
46
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187 ]:
77
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188 default_session_data[assref_name]["visibility"]["default_on"].append(key)
35
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189 else:
77
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190 default_session_data[assref_name]["visibility"]["default_off"].append(
46
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191 key
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192 )
60
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193 if trext in ["gff", "gff3", "bed", "vcf", "maf", "blastxml"]:
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194 ttype = "LinearBasicDisplay"
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195 if trext == "vcf":
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196 ttype = "LinearVariantDisplay"
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197 style_json = {
67
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198 "type": ttype,
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199 "trackShowLabels": False,
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200 "trackShowDescriptions": False,
60
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201 }
77
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202 default_session_data[assref_name]["style"][key] = style_json
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203 default_session_data[assref_name]["tracks"].append(key)
30
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204 # general_data = {
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205 # "analytics": root.find("metadata/general/analytics").text,
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206 # "primary_color": root.find("metadata/general/primary_color").text,
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207 # "secondary_color": root.find("metadata/general/secondary_color").text,
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208 # "tertiary_color": root.find("metadata/general/tertiary_color").text,
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209 # "quaternary_color": root.find("metadata/general/quaternary_color").text,
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210 # "font_size": root.find("metadata/general/font_size").text,
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211 # }
66
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212 jc.add_general_configuration({})
65
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213 trackconf = jc.config_json.get("tracks", [])
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214 for gnome in jc.genome_names:
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215 trackconf += jc.tracksToAdd[gnome]
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216 logging.debug(
69
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217 "++++ adding trackconf=%s for gnome %s" % (trackconf, gnome)
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218 )
65
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219 jc.config_json["tracks"] = trackconf
69
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220 assconf = jc.config_json.get("assemblies", [])
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221 assconf += jc.assemblies
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222 jc.config_json["assemblies"] = assconf
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223 logging.debug("+++assemblies=%s, gnames=%s" % (assconf, jc.genome_names))
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224 jc.write_config()
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225 default_session_data.update({"session_name": sessName})
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226 track_conf.update(default_session_data)
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227 jc.add_default_session(default_session_data)
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228 # jc.add_defsess_to_index(default_session_data)
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229 # jc.text_index() not sure what broke here.
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230 else:
46
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231 sys.stderr.write(
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232 "Please add a fasta genome reference to the collection. No suitable reference fasta for autogenJB2 - nothing to process"
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233 )