Mercurial > repos > fubar > jbrowse2

annotate autogenJB2.py @ 97:74074746ccd8 draft

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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
author fubar
date Sat, 01 Jun 2024 05:37:13 +0000
parents 4c517a0041a8
children b1260bca5fdc
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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 logging.debug("@@@autogenJB2 paths=%s, genomes=%s" % (genome_paths, genomes))
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81 assref_name = jc.process_genomes(genomes[0])
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82 if not default_session_data.get(assref_name, None):
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83 default_session_data[assref_name] = {
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84 "tracks": [],
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85 "style": {},
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86 "style_labels": {},
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87 "visibility": {
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88 "default_on": [],
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89 "default_off": [],
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90 },
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91 }
35
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92 listtracks = trackList
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93 tnames = [x[2] for x in listtracks]
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94 texts = [x[1] for x in listtracks]
30
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95 for i, track in enumerate(listtracks):
67
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96 track_conf = {
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97 "trackfiles": [],
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98 "category": "autogenerated",
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99 "assemblyNames": assref_name,
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100 }
35
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101 tpath, trext, trackname = track[:3]
48
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102 track_conf["dataset_id"] = trackname
52
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103 useuri = "no"
57
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104 if tpath.startswith("http://") or tpath.startswith("https://"):
52
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105 useuri = "yes"
35
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106 if trext == "paf":
97
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107 refdat = ["%s ~ %s" % (x[0],x[2]) for x in listtracks if x[1] in ["fasta", "fasta.gz"]]
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108 if len(refdat) == 0:
30
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109 jc.logging.warn(
97
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110 "!! No reference file for %s found. Using main reference"
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111 % (refname)
30
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112 )
97
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113 refdat = ["%s ~ %s" % (genomes[0].path, assref_name),]
30
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114 else:
57
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115 track_conf.update(
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116 {
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117 "conf": {
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118 "options": {
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119 "paf": {
97
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120 "genome": ",".join(refdat)
57
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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":
57
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127 ipath = track[3]
46
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128 if not os.path.exists(ipath):
57
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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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diff changeset
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(
93
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143 {"conf": {"options": {"bam": {"bam_index": " %s ~ %s," % (tpath,ipath)}}}}
57
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144 )
46
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145 elif trext == "cram":
57
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146 ipath = track[3]
46
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147 if not os.path.exists(ipath):
57
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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(
93
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diff changeset
161 {"conf": {"options": {"cram": {"cram_index": "%s ~ %s," % (tpath, ipath)}}}}
57
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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",
72
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178 "bed",
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179 "hic"
46
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180 ]:
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181 default_session_data[assref_name]["visibility"]["default_on"].append(key)
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182 else:
77
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183 default_session_data[assref_name]["visibility"]["default_off"].append(
46
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184 key
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185 )
60
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186 if trext in ["gff", "gff3", "bed", "vcf", "maf", "blastxml"]:
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187 ttype = "LinearBasicDisplay"
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188 if trext == "vcf":
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189 ttype = "LinearVariantDisplay"
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190 style_json = {
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191 "type": ttype,
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192 "trackShowLabels": False,
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193 "trackShowDescriptions": False,
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194 }
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195 default_session_data[assref_name]["style"][key] = style_json
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196 default_session_data[assref_name]["tracks"].append(key)
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197 # general_data = {
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198 # "analytics": root.find("metadata/general/analytics").text,
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199 # "primary_color": root.find("metadata/general/primary_color").text,
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200 # "secondary_color": root.find("metadata/general/secondary_color").text,
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201 # "tertiary_color": root.find("metadata/general/tertiary_color").text,
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202 # "quaternary_color": root.find("metadata/general/quaternary_color").text,
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203 # "font_size": root.find("metadata/general/font_size").text,
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204 # }
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205 jc.add_general_configuration({})
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206 trackconf = jc.config_json.get("tracks", [])
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207 for gnome in jc.genome_names:
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208 trackconf += jc.tracksToAdd[gnome]
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209 logging.debug(
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210 "++++ adding trackconf=%s for gnome %s" % (trackconf, gnome)
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211 )
65
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212 jc.config_json["tracks"] = trackconf
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213 assconf = jc.config_json.get("assemblies", [])
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214 assconf += jc.assemblies
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215 jc.config_json["assemblies"] = assconf
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216 logging.debug("+++assemblies=%s, gnames=%s" % (assconf, jc.genome_names))
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217 jc.write_config()
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218 default_session_data.update({"session_name": sessName})
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219 track_conf.update(default_session_data)
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220 jc.add_default_session(default_session_data)
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221 # jc.add_defsess_to_index(default_session_data)
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222 # jc.text_index() not sure what broke here.
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223 else:
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224 sys.stderr.write(
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225 "!!!! Collection has no suitable trackfiles for autogenJB2 - nothing to process"
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226 )