Mercurial > repos > fubar > jbrowse2

comparison autogenJB2.py @ 67:cefe9dbf1d80 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 6dac6d6debf44c68eae2785e926fb8420f76958e-dirty
author fubar
date Thu, 28 Mar 2024 12:17:24 +0000
parents bc10ad1dfb98
children 7230a2422507
comparison
equal deleted inserted replaced
66:bc10ad1dfb98 67:cefe9dbf1d80
3 import os 3 import os
4 import sys 4 import sys
5 5
6 from jbrowse2 import JbrowseConnector as jbC 6 from jbrowse2 import JbrowseConnector as jbC
7 7
8 logging.basicConfig(level=logging.debug) 8
9 logging.basicConfig(level=logging.DEBUG)
9 log = logging.getLogger("jbrowse") 10 log = logging.getLogger("jbrowse")
10
11 11
12 if __name__ == "__main__": 12 if __name__ == "__main__":
13 parser = argparse.ArgumentParser(description="", epilog="") 13 parser = argparse.ArgumentParser(description="", epilog="")
14 parser.add_argument("--sessName", help="Session name", default="AutoJBrowse") 14 parser.add_argument("--sessName", help="Session name", default="AutoJBrowse")
15 parser.add_argument( 15 parser.add_argument(
60 guseuri.append("no") 60 guseuri.append("no")
61 jc = jbC( 61 jc = jbC(
62 outdir=args.outdir, 62 outdir=args.outdir,
63 jbrowse2path=args.jbrowse2path, 63 jbrowse2path=args.jbrowse2path,
64 ) 64 )
65 genomes=[ 65 genomes = (
66 [
66 { 67 {
67 "path": x, 68 "path": x,
68 "label": genome_names[i], 69 "label": genome_names[i],
69 "useuri": guseuri[i], 70 "useuri": guseuri[i],
70 "meta": { 71 "meta": {
72 "dataset_dname": genome_names[i], 73 "dataset_dname": genome_names[i],
73 }, 74 },
74 } 75 }
75 for i, x in enumerate(genome_paths) 76 for i, x in enumerate(genome_paths)
76 ], 77 ],
78 )
77 logging.warn("#!!! paths=%s, genomes=%s" % (genome_paths, genomes)) 79 logging.warn("#!!! paths=%s, genomes=%s" % (genome_paths, genomes))
78 assref_name = jc.process_genomes(genomes[0]) 80 assref_name = jc.process_genomes(genomes[0])
79 default_session_data = { 81 default_session_data = {
80 "visibility": { 82 "visibility": {
81 "default_on": [], 83 "default_on": [],
87 listtracks = trackList 89 listtracks = trackList
88 # foo.paf must have a foo_paf.fasta or fasta.gz to match 90 # foo.paf must have a foo_paf.fasta or fasta.gz to match
89 tnames = [x[2] for x in listtracks] 91 tnames = [x[2] for x in listtracks]
90 texts = [x[1] for x in listtracks] 92 texts = [x[1] for x in listtracks]
91 for i, track in enumerate(listtracks): 93 for i, track in enumerate(listtracks):
92 track_conf = {"trackfiles": [], "category": "autogenerated", "assemblyNames": assref_name} 94 track_conf = {
95 "trackfiles": [],
96 "category": "autogenerated",
97 "assemblyNames": assref_name,
98 }
93 tpath, trext, trackname = track[:3] 99 tpath, trext, trackname = track[:3]
94 track_conf["dataset_id"] = trackname 100 track_conf["dataset_id"] = trackname
95 useuri = "no" 101 useuri = "no"
96 if tpath.startswith("http://") or tpath.startswith("https://"): 102 if tpath.startswith("http://") or tpath.startswith("https://"):
97 useuri = "yes" 103 useuri = "yes"
163 169
164 if keys: 170 if keys:
165 for key in keys: 171 for key in keys:
166 if trext in [ 172 if trext in [
167 "bigwig", 173 "bigwig",
168 "gff", "gff3", 174 "gff",
175 "gff3",
169 "vcf", 176 "vcf",
170 "maf", 177 "maf",
171 ]: 178 ]:
172 default_session_data["visibility"]["default_on"].append(key) 179 default_session_data["visibility"]["default_on"].append(key)
173 else: 180 else:
177 if trext in ["gff", "gff3", "bed", "vcf", "maf", "blastxml"]: 184 if trext in ["gff", "gff3", "bed", "vcf", "maf", "blastxml"]:
178 ttype = "LinearBasicDisplay" 185 ttype = "LinearBasicDisplay"
179 if trext == "vcf": 186 if trext == "vcf":
180 ttype = "LinearVariantDisplay" 187 ttype = "LinearVariantDisplay"
181 style_json = { 188 style_json = {
182 "type": ttype, 189 "type": ttype,
183 "trackShowLabels": False, 190 "trackShowLabels": False,
184 "trackShowDescriptions": False 191 "trackShowDescriptions": False,
185 } 192 }
186 default_session_data["style"][key] = style_json 193 default_session_data["style"][key] = style_json
187 # general_data = { 194 # general_data = {
188 # "analytics": root.find("metadata/general/analytics").text, 195 # "analytics": root.find("metadata/general/analytics").text,
189 # "primary_color": root.find("metadata/general/primary_color").text, 196 # "primary_color": root.find("metadata/general/primary_color").text,
194 # } 201 # }
195 jc.add_general_configuration({}) 202 jc.add_general_configuration({})
196 trackconf = jc.config_json.get("tracks", []) 203 trackconf = jc.config_json.get("tracks", [])
197 for gnome in jc.genome_names: 204 for gnome in jc.genome_names:
198 trackconf += jc.tracksToAdd[gnome] 205 trackconf += jc.tracksToAdd[gnome]
206 logging.warn(
207 "^^%% adding trackconf=%s for gnome %s" % (trackconf, gnome)
208 )
199 jc.config_json["tracks"] = trackconf 209 jc.config_json["tracks"] = trackconf
200 jc.write_config() 210 jc.write_config()
201 default_session_data.update( 211 default_session_data.update({"session_name": sessName})
202 {"session_name": sessName}
203 )
204 track_conf.update(default_session_data) 212 track_conf.update(default_session_data)
205 jc.add_default_session(default_session_data) 213 jc.add_default_session(default_session_data)
206 # jc.text_index() not sure what broke here. 214 # jc.text_index() not sure what broke here.
207 else: 215 else:
208 sys.stderr.write( 216 sys.stderr.write(
209 "!!!! Collection has no suitable trackfiles for autogenJB2 - nothing to process" 217 "!!!! Collection has no suitable trackfiles for autogenJB2 - nothing to process"
210 ) 218 )
211