Mercurial > repos > fubar > jbrowse2
comparison autogenJB2.py @ 77:3dcda36b97b4 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit d03454f949af9f3fff638f6a3e52fe42bc96be3b-dirty
| author | fubar |
|---|---|
| date | Mon, 01 Apr 2024 04:35:23 +0000 |
| parents | 2bdb748df098 |
| children | 5c295cc220ed |
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| 76:9e3eb6b26f85 | 77:3dcda36b97b4 |
|---|---|
| 41 ) | 41 ) |
| 42 parser.add_argument("--outdir", help="Output directory", required=True) | 42 parser.add_argument("--outdir", help="Output directory", required=True) |
| 43 parser.add_argument("--version", "-V", action="version", version="%(prog)s 2.10.2") | 43 parser.add_argument("--version", "-V", action="version", version="%(prog)s 2.10.2") |
| 44 args = parser.parse_args() | 44 args = parser.parse_args() |
| 45 sessName = args.sessName | 45 sessName = args.sessName |
| 46 default_session_data = {} | |
| 46 # --trackmeta $jbrowseme[$key],$jbrowseme[$key].ext,'$key' | 47 # --trackmeta $jbrowseme[$key],$jbrowseme[$key].ext,'$key' |
| 47 trackList = [x.strip().split(",") for x in args.trackmeta if x > ""] | 48 trackList = [x.strip().split(",") for x in args.trackmeta if x > ""] |
| 48 refList = [x.strip().split(",") for x in args.referencemeta if x > ""] | 49 refList = [x.strip().split(",") for x in args.referencemeta if x > ""] |
| 49 if len(refList) > 0: | 50 if len(refList) > 0: |
| 50 listgenomes = [f for f in refList if f[1] in ["fasta", "fasta.gz"]] | 51 listgenomes = [f for f in refList if f[1] in ["fasta", "fasta.gz"]] |
| 74 }, | 75 }, |
| 75 } | 76 } |
| 76 for i, x in enumerate(genome_paths) | 77 for i, x in enumerate(genome_paths) |
| 77 ], | 78 ], |
| 78 ) | 79 ) |
| 79 logging.debug("#!!! paths=%s, genomes=%s" % (genome_paths, genomes)) | 80 logging.debug("@@@ paths=%s, genomes=%s" % (genome_paths, genomes)) |
| 80 assref_name = jc.process_genomes(genomes[0]) | 81 assref_name = jc.process_genomes(genomes[0]) |
| 81 default_session_data = { | 82 if not default_session_data.get(assref_name, None): |
| 82 "visibility": { | 83 default_session_data[assref_name] = { |
| 83 "default_on": [], | 84 "tracks": [], |
| 84 "default_off": [], | 85 "style": {}, |
| 85 }, | 86 "style_labels": {}, |
| 86 "style": {}, | 87 "visibility": { |
| 87 "style_labels": {}, | 88 "default_on": [], |
| 88 } | 89 "default_off": [], |
| 90 }, | |
| 91 } | |
| 89 listtracks = trackList | 92 listtracks = trackList |
| 90 # foo.paf must have a foo_paf.fasta or fasta.gz to match | 93 # foo.paf must have a foo_paf.fasta or fasta.gz to match |
| 91 tnames = [x[2] for x in listtracks] | 94 tnames = [x[2] for x in listtracks] |
| 92 texts = [x[1] for x in listtracks] | 95 texts = [x[1] for x in listtracks] |
| 93 for i, track in enumerate(listtracks): | 96 for i, track in enumerate(listtracks): |
| 176 "vcf", | 179 "vcf", |
| 177 "maf", | 180 "maf", |
| 178 "bed", | 181 "bed", |
| 179 "hic" | 182 "hic" |
| 180 ]: | 183 ]: |
| 181 default_session_data["visibility"]["default_on"].append(key) | 184 default_session_data[assref_name]["visibility"]["default_on"].append(key) |
| 182 else: | 185 else: |
| 183 default_session_data["visibility"]["default_off"].append( | 186 default_session_data[assref_name]["visibility"]["default_off"].append( |
| 184 key | 187 key |
| 185 ) | 188 ) |
| 186 if trext in ["gff", "gff3", "bed", "vcf", "maf", "blastxml"]: | 189 if trext in ["gff", "gff3", "bed", "vcf", "maf", "blastxml"]: |
| 187 ttype = "LinearBasicDisplay" | 190 ttype = "LinearBasicDisplay" |
| 188 if trext == "vcf": | 191 if trext == "vcf": |
| 190 style_json = { | 193 style_json = { |
| 191 "type": ttype, | 194 "type": ttype, |
| 192 "trackShowLabels": False, | 195 "trackShowLabels": False, |
| 193 "trackShowDescriptions": False, | 196 "trackShowDescriptions": False, |
| 194 } | 197 } |
| 195 default_session_data["style"][key] = style_json | 198 default_session_data[assref_name]["style"][key] = style_json |
| 199 default_session_data[assref_name]["tracks"].append(key) | |
| 196 # general_data = { | 200 # general_data = { |
| 197 # "analytics": root.find("metadata/general/analytics").text, | 201 # "analytics": root.find("metadata/general/analytics").text, |
| 198 # "primary_color": root.find("metadata/general/primary_color").text, | 202 # "primary_color": root.find("metadata/general/primary_color").text, |
| 199 # "secondary_color": root.find("metadata/general/secondary_color").text, | 203 # "secondary_color": root.find("metadata/general/secondary_color").text, |
| 200 # "tertiary_color": root.find("metadata/general/tertiary_color").text, | 204 # "tertiary_color": root.find("metadata/general/tertiary_color").text, |
| 214 jc.config_json["assemblies"] = assconf | 218 jc.config_json["assemblies"] = assconf |
| 215 logging.debug("+++assemblies=%s, gnames=%s" % (assconf, jc.genome_names)) | 219 logging.debug("+++assemblies=%s, gnames=%s" % (assconf, jc.genome_names)) |
| 216 jc.write_config() | 220 jc.write_config() |
| 217 default_session_data.update({"session_name": sessName}) | 221 default_session_data.update({"session_name": sessName}) |
| 218 track_conf.update(default_session_data) | 222 track_conf.update(default_session_data) |
| 219 jc.add_default_session(default_session_data) | 223 # jc.add_default_session(default_session_data) |
| 224 jc.add_defsess_to_index(default_session_data) | |
| 220 # jc.text_index() not sure what broke here. | 225 # jc.text_index() not sure what broke here. |
| 221 else: | 226 else: |
| 222 sys.stderr.write( | 227 sys.stderr.write( |
| 223 "!!!! Collection has no suitable trackfiles for autogenJB2 - nothing to process" | 228 "!!!! Collection has no suitable trackfiles for autogenJB2 - nothing to process" |
| 224 ) | 229 ) |