Mercurial > repos > fubar > jbrowse2

annotate autogenJB2.py @ 39:bc57164eb270 draft

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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit ace841acd53be99494ed9bba8bb9e2ae212d3661
author fubar
date Fri, 01 Mar 2024 01:03:09 +0000
parents 07849bf248e3
children 4181e97c70a7
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1 import argparse
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2 import logging
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3 import sys
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4
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5 from jbrowse2 import JbrowseConnector as jbC
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7 logging.basicConfig(level=logging.debug)
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8 log = logging.getLogger("jbrowse")
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10
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11 def makeDefaultLocation():
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12
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13 refName = jc.genome_firstcontig
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14 defloc = "%s:100..10000" % refName
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15 print ('defloc',defloc)
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16 return defloc
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19 if __name__ == "__main__":
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20 parser = argparse.ArgumentParser(description="", epilog="")
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21 parser.add_argument("--sessName", help="Session name", default="AutoJBrowse")
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22 parser.add_argument(
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23 "--trackmeta",
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24 help="Repeatable of 'filename, filext,filepath, ... ,' for JBrowse2 tracks",
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25 default=[],
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26 action="append",
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27 )
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28 parser.add_argument(
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29 "--referencemeta",
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30 help="Repeatable 'filename, filext, filepath, ... ,' for JBrowse2 reference tracks",
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31 default=[],
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32 action="append",
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33 )
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34 parser.add_argument(
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35 "--pafmeta",
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36 help="Repeatable. Each is a 'filename, filext, filepath, ... ,' for a JBrowse2 paf track",
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37 default=[],
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38 action="append",
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39 )
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40 parser.add_argument(
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41 "--pafreferencemeta",
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42 help="Repeatable. Each is a 'pafname,filepath,refname,filepath,refname....'. Every paf must have a corresponding one ",
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43 default=[],
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44 action="append",
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45 )
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46 parser.add_argument("--jbrowse2path", help="Path to JBrowse2 directory in biocontainer or Conda")
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47 parser.add_argument("--outdir", help="Output directory", required=True)
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48 parser.add_argument("--version", "-V", action="version", version="%(prog)s 2.10.2")
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49 args = parser.parse_args()
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50 sessName = args.sessName
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51 # --trackmeta $jbrowseme[$key],$jbrowseme[$key].ext,'$key'
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52 trackList = [x.strip().split(",") for x in args.trackmeta if x > '']
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53 refList = [x.strip().split(",") for x in args.referencemeta if x > '']
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54 print("tracklist = %s\nreflist = %s" % (trackList,refList))
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55 if len(refList) > 0:
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56 listgenomes = [f for f in refList if f[1] in ['fasta', 'fasta.gz']]
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57 # assume no pafs here
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58 print('genomes=%s' % listgenomes)
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59 if len(listgenomes) > 0:
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60 genome_paths = [
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61 x[0] for x in listgenomes
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62 ] # expect genome_1_genomename.fasta etc
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63 genome_names = [x[2] for x in listgenomes]
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64 jc = jbC(
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65 outdir=args.outdir,
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66 jbrowse2path=args.jbrowse2path,
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67 genomes=[
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68 {
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69 "path": x,
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70 "meta": {
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71 "name": genome_names[i],
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72 "dataset_dname": genome_names[i],
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73 },
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74 }
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75 for i, x in enumerate(genome_paths)
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76 ],
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77 )
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78 sys.stdout.write('$$$ genome_paths:%s genome_names: %s' % (genome_paths,genome_names))
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79 jc.process_genomes()
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80 default_session_data = {
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81 "visibility": {
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82 "default_on": [],
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83 "default_off": [],
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84 },
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85 "style": {},
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86 "style_labels": {},
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87 }
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88
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89 listtracks = trackList
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90 # foo.paf must have a foo_paf.fasta or fasta.gz to match
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91 tnames = [x[2] for x in listtracks]
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92 texts = [x[1] for x in listtracks]
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93 for i, track in enumerate(listtracks):
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94 tpath, trext, trackname = track[:3]
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95 if trext == "paf":
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96 refname = trackname + "_paf.fasta"
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97 refdat = [x[2] for x in listtracks if x[2] == refname]
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98 if not refdat:
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99 jc.logging.warn(
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100 "!! 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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101 % (refname, trackname)
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102 )
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103 sys.exit(3)
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104 else:
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105 track_conf = {
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106 "conf": {
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107 "options": {
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108 "paf": {"genome": refdat, "genome_label": trackname}
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109 }
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110 }
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111 }
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112 elif trext == 'bam':
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113 track_conf = {"conf": {"options": {"bam": {"bam_index": track[3]}}}}
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114 elif trext == 'cram':
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115 track_conf = {"conf": {"options": {"cram": {"cram_index": track[3]}}}}
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116 else:
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117 track_conf = {}
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118 track_conf["format"] = trext
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119 track_conf["name"] = trackname
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120 track_conf["label"] = trackname
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121 track_conf["trackfiles"] = [(tpath, trext, trackname,{}),]
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122 track_conf["category"] = "Autogenerated"
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123 keys = jc.process_annotations(track_conf)
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124
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125 if keys:
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126 for key in keys:
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127 if trext in ["bigwig", "gff3", "gff", "vcf", "maf",]:
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128 default_session_data["visibility"]["default_on"].append(key)
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129 else:
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130 default_session_data["visibility"]["default_off"].append(key)
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131 # if track_conf.get("style", None):
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132 # default_session_data["style"][key] = track_conf[
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133 # "style"
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134 # ] # TODO do we need this anymore?
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135 # if track_conf.get("style_lables", None):
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136 # default_session_data["style_labels"][key] = track_conf.get(
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137 # "style_labels", None
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138 # )
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139 # general_data = {
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140 # "analytics": root.find("metadata/general/analytics").text,
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141 # "primary_color": root.find("metadata/general/primary_color").text,
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142 # "secondary_color": root.find("metadata/general/secondary_color").text,
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143 # "tertiary_color": root.find("metadata/general/tertiary_color").text,
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144 # "quaternary_color": root.find("metadata/general/quaternary_color").text,
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145 # "font_size": root.find("metadata/general/font_size").text,
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146 # }
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147 # jc.add_general_configuration(general_data)
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148 trackconf = jc.config_json.get("tracks", None)
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149 if trackconf:
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150 jc.config_json["tracks"].update(jc.tracksToAdd)
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151 else:
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152 jc.config_json["tracks"] = jc.tracksToAdd
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153 jc.write_config()
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154 defLoc = makeDefaultLocation()
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155 default_session_data.update({"defaultLocation": defLoc, "session_name": sessName})
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156 track_conf.update(default_session_data)
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157 jc.add_default_session(default_session_data)
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158 # jc.text_index() not sure what broke here.
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159 else:
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160 print("!! empty collection supplied - nothing to process")