Mercurial > repos > fubar > jbrowse2

annotate autogenJB2.py @ 70:5f0ee87daef4 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit aacbae2ec1bf5c69017c37f925c9d400e8a8ba9d-dirty
author fubar
date Fri, 29 Mar 2024 09:35:57 +0000
parents 7230a2422507
children e26a8a6d2d2e
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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 # --trackmeta $jbrowseme[$key],$jbrowseme[$key].ext,'$key'
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47 trackList = [x.strip().split(",") for x in args.trackmeta if x > ""]
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48 refList = [x.strip().split(",") for x in args.referencemeta if x > ""]
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49 if len(refList) > 0:
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50 listgenomes = [f for f in refList if f[1] in ["fasta", "fasta.gz"]]
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51 # assume no pafs here
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52 if len(listgenomes) > 0:
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53 genome_paths = [x[0] for x in listgenomes]
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54 genome_names = [x[2] for x in listgenomes]
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55 guseuri = []
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56 for x in genome_paths:
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57 if x.startswith("http://") or x.startswith("https://"):
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58 guseuri.append("yes")
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59 else:
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60 guseuri.append("no")
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61 jc = jbC(
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62 outdir=args.outdir,
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63 jbrowse2path=args.jbrowse2path,
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64 )
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65 genomes = (
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66 [
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67 {
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68 "path": x,
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69 "label": genome_names[i],
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70 "useuri": guseuri[i],
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71 "meta": {
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72 "name": genome_names[i],
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73 "dataset_dname": genome_names[i],
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74 },
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75 }
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76 for i, x in enumerate(genome_paths)
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77 ],
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78 )
62
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79 logging.warn("#!!! paths=%s, genomes=%s" % (genome_paths, genomes))
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80 assref_name = jc.process_genomes(genomes[0])
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81 default_session_data = {
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82 "visibility": {
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83 "default_on": [],
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84 "default_off": [],
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85 },
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86 "style": {},
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87 "style_labels": {},
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88 }
35
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89 listtracks = trackList
30
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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):
67
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94 track_conf = {
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95 "trackfiles": [],
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96 "category": "autogenerated",
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97 "assemblyNames": assref_name,
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98 }
35
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99 tpath, trext, trackname = track[:3]
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100 track_conf["dataset_id"] = trackname
52
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101 useuri = "no"
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102 if tpath.startswith("http://") or tpath.startswith("https://"):
52
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103 useuri = "yes"
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104 if trext == "paf":
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105 refname = trackname + "_paf.fasta"
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106 refdat = [x[2] for x in listtracks if x[2] == refname]
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107 if not refdat:
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108 jc.logging.warn(
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109 "!! No reference file %s corresponding to paf file %s found. Not building - there must be a corresponding fasta for each paf"
35
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110 % (refname, trackname)
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111 )
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112 sys.exit(3)
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113 else:
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114 track_conf.update(
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115 {
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116 "conf": {
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117 "options": {
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118 "paf": {
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119 "genome": refdat,
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120 "genome_label": trackname,
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121 }
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122 }
30
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123 }
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124 }
57
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125 )
46
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126 elif trext == "bam":
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127 ipath = track[3]
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128 if not os.path.exists(ipath):
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129 ipath = os.path.realpath(
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130 os.path.join(jc.outdir, trackname + ".bai")
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131 )
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132 cmd = [
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133 "samtools",
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134 "index",
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135 "-b",
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136 "-o",
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137 ipath,
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138 os.path.realpath(track[0]),
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139 ]
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140 sys.stdout.write("#### calling %s" % " ".join(cmd))
46
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141 jc.subprocess_check_call(cmd)
57
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142 track_conf.update(
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143 {"conf": {"options": {"bam": {"bam_index": ipath}}}}
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144 )
46
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145 elif trext == "cram":
57
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146 ipath = track[3]
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147 if not os.path.exists(ipath):
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148 ipath = os.path.realpath(
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149 os.path.join("./", trackname + ".crai")
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150 )
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151 cmd = [
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152 "samtools",
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153 "index",
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154 "-c",
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155 "-o",
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156 ipath,
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157 os.path.realpath(track[0]),
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158 ]
46
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159 jc.subprocess_check_call(cmd)
57
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160 track_conf.update(
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161 {"conf": {"options": {"cram": {"cram_index": ipath}}}}
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162 )
48
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163 track_conf["path"] = tpath
35
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164 track_conf["format"] = trext
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165 track_conf["name"] = trackname
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166 track_conf["label"] = trackname
52
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167 track_conf["trackfiles"].append((tpath, trext, useuri, trackname, {}))
30
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168 keys = jc.process_annotations(track_conf)
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169
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170 if keys:
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171 for key in keys:
46
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172 if trext in [
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173 "bigwig",
67
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174 "gff",
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175 "gff3",
46
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176 "vcf",
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177 "maf",
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178 ]:
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179 default_session_data["visibility"]["default_on"].append(key)
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180 else:
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181 default_session_data["visibility"]["default_off"].append(
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182 key
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183 )
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184 if trext in ["gff", "gff3", "bed", "vcf", "maf", "blastxml"]:
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185 ttype = "LinearBasicDisplay"
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186 if trext == "vcf":
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187 ttype = "LinearVariantDisplay"
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188 style_json = {
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189 "type": ttype,
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190 "trackShowLabels": False,
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191 "trackShowDescriptions": False,
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192 }
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193 default_session_data["style"][key] = style_json
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194 # general_data = {
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195 # "analytics": root.find("metadata/general/analytics").text,
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196 # "primary_color": root.find("metadata/general/primary_color").text,
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197 # "secondary_color": root.find("metadata/general/secondary_color").text,
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198 # "tertiary_color": root.find("metadata/general/tertiary_color").text,
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199 # "quaternary_color": root.find("metadata/general/quaternary_color").text,
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200 # "font_size": root.find("metadata/general/font_size").text,
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201 # }
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202 jc.add_general_configuration({})
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203 trackconf = jc.config_json.get("tracks", [])
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204 for gnome in jc.genome_names:
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205 trackconf += jc.tracksToAdd[gnome]
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206 logging.warn(
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207 "++++ adding trackconf=%s for gnome %s" % (trackconf, gnome)
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208 )
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209 jc.config_json["tracks"] = trackconf
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210 assconf = jc.config_json.get("assemblies", [])
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211 assconf += jc.assemblies
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212 jc.config_json["assemblies"] = assconf
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213 logging.warn("+++assemblies=%s, gnames=%s" % (assconf, jc.genome_names))
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214 jc.write_config()
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215 default_session_data.update({"session_name": sessName})
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216 track_conf.update(default_session_data)
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217 jc.add_default_session(default_session_data)
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218 # jc.text_index() not sure what broke here.
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219 else:
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220 sys.stderr.write(
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221 "!!!! Collection has no suitable trackfiles for autogenJB2 - nothing to process"
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222 )