Mercurial > repos > fubar > jbrowse2

annotate autogenJB2.py @ 60:81d535970196 draft

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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 403a35e1245fa5e62f4be6116a725b9e4d9c353a
author fubar
date Mon, 25 Mar 2024 02:10:05 +0000
parents 94264fe60478
children ab0d6782a95f
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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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8 logging.basicConfig(level=logging.debug)
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9 log = logging.getLogger("jbrowse")
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11
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12 def makeDefaultLocation():
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13
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14 refName = jc.genome_firstcontig
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15 defloc = "%s:100..10000" % refName
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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 'filename,filext,filepath,[bai/crai path for filesystem bam/cram]' 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 - usually only one needed",
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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 'pafname, 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,refpath,refname' Every pafname must have one or more",
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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(
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47 "--jbrowse2path", help="Path to JBrowse2 directory in biocontainer or Conda"
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48 )
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49 parser.add_argument("--outdir", help="Output directory", required=True)
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50 parser.add_argument("--version", "-V", action="version", version="%(prog)s 2.10.2")
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51 args = parser.parse_args()
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52 sessName = args.sessName
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53 # --trackmeta $jbrowseme[$key],$jbrowseme[$key].ext,'$key'
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54 trackList = [x.strip().split(",") for x in args.trackmeta if x > ""]
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55 refList = [x.strip().split(",") for x in args.referencemeta if x > ""]
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56 if len(refList) > 0:
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57 listgenomes = [f for f in refList if f[1] in ["fasta", "fasta.gz"]]
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58 # assume no pafs here
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59 if len(listgenomes) > 0:
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60 genome_paths = [x[0] for x in listgenomes]
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61 genome_names = [x[2] for x in listgenomes]
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62 guseuri = []
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63 for x in genome_paths:
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64 if x.startswith("http://") or x.startswith("https://"):
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65 guseuri.append("yes")
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66 else:
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67 guseuri.append("no")
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68 jc = jbC(
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69 outdir=args.outdir,
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70 jbrowse2path=args.jbrowse2path,
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71 genomes=[
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72 {
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73 "path": x,
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74 "label": genome_names[i],
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75 "useuri": guseuri[i],
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76 "meta": {
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77 "name": genome_names[i],
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78 "dataset_dname": genome_names[i],
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79 },
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80 }
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81 for i, x in enumerate(genome_paths)
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82 ],
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83 )
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84
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85 jc.process_genomes()
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86 default_session_data = {
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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 "style": {},
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92 "style_labels": {},
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93 }
35
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94 listtracks = trackList
30
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95 # foo.paf must have a foo_paf.fasta or fasta.gz to match
35
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96 tnames = [x[2] for x in listtracks]
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97 texts = [x[1] for x in listtracks]
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98 for i, track in enumerate(listtracks):
52
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99 track_conf = {"trackfiles": [], "category": "autogenerated"}
35
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100 tpath, trext, trackname = track[:3]
48
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101 track_conf["dataset_id"] = trackname
52
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102 useuri = "no"
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103 if tpath.startswith("http://") or tpath.startswith("https://"):
52
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104 useuri = "yes"
35
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105 if trext == "paf":
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106 refname = trackname + "_paf.fasta"
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107 refdat = [x[2] for x in listtracks if x[2] == refname]
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108 if not refdat:
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109 jc.logging.warn(
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110 "!! 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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111 % (refname, trackname)
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112 )
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113 sys.exit(3)
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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": {
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120 "genome": refdat,
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121 "genome_label": trackname,
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122 }
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123 }
30
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124 }
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125 }
57
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126 )
46
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127 elif trext == "bam":
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128 ipath = track[3]
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129 if not os.path.exists(ipath):
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130 ipath = os.path.realpath(
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131 os.path.join(jc.outdir, trackname + ".bai")
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132 )
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133 cmd = [
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134 "samtools",
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135 "index",
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136 "-b",
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137 "-o",
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138 ipath,
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139 os.path.realpath(track[0]),
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140 ]
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141 sys.stdout.write("#### calling %s" % " ".join(cmd))
46
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142 jc.subprocess_check_call(cmd)
57
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143 track_conf.update(
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144 {"conf": {"options": {"bam": {"bam_index": ipath}}}}
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145 )
46
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146 elif trext == "cram":
57
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147 ipath = track[3]
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148 if not os.path.exists(ipath):
57
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149 ipath = os.path.realpath(
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150 os.path.join("./", trackname + ".crai")
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151 )
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152 cmd = [
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153 "samtools",
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154 "index",
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155 "-c",
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156 "-o",
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157 ipath,
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158 os.path.realpath(track[0]),
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159 ]
46
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160 jc.subprocess_check_call(cmd)
57
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161 track_conf.update(
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162 {"conf": {"options": {"cram": {"cram_index": ipath}}}}
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163 )
48
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164 track_conf["path"] = tpath
35
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165 track_conf["format"] = trext
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166 track_conf["name"] = trackname
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167 track_conf["label"] = trackname
52
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168 track_conf["trackfiles"].append((tpath, trext, useuri, trackname, {}))
30
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169 keys = jc.process_annotations(track_conf)
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170
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171 if keys:
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172 for key in keys:
46
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173 if trext in [
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174 "bigwig",
60
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175 "gff", "gff3",
46
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176 "vcf",
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177 "maf",
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178 ]:
35
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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
30
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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(general_data)
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203 trackconf = jc.config_json.get("tracks", None)
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204 if trackconf:
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205 jc.config_json["tracks"].update(jc.tracksToAdd)
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206 else:
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207 jc.config_json["tracks"] = jc.tracksToAdd
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208 jc.write_config()
35
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209 defLoc = makeDefaultLocation()
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210 default_session_data.update(
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211 {"defaultLocation": defLoc, "session_name": sessName}
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212 )
35
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213 track_conf.update(default_session_data)
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214 jc.add_default_session(default_session_data)
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215 # jc.text_index() not sure what broke here.
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216 else:
46
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217 sys.stderr.write(
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218 "!!!! Collection has no suitable trackfiles for autogenJB2 - nothing to process"
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219 )