Mercurial > repos > fubar > jbrowse2
comparison autogenJB2.py @ 97:74074746ccd8 draft
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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| 96:5ef1ba2031f2 | 97:74074746ccd8 |
|---|---|
| 75 }, | 75 }, |
| 76 } | 76 } |
| 77 for i, x in enumerate(genome_paths) | 77 for i, x in enumerate(genome_paths) |
| 78 ], | 78 ], |
| 79 ) | 79 ) |
| 80 logging.debug("@@@ paths=%s, genomes=%s" % (genome_paths, genomes)) | 80 logging.debug("@@@autogenJB2 paths=%s, genomes=%s" % (genome_paths, genomes)) |
| 81 assref_name = jc.process_genomes(genomes[0]) | 81 assref_name = jc.process_genomes(genomes[0]) |
| 82 if not default_session_data.get(assref_name, None): | 82 if not default_session_data.get(assref_name, None): |
| 83 default_session_data[assref_name] = { | 83 default_session_data[assref_name] = { |
| 84 "tracks": [], | 84 "tracks": [], |
| 85 "style": {}, | 85 "style": {}, |
| 88 "default_on": [], | 88 "default_on": [], |
| 89 "default_off": [], | 89 "default_off": [], |
| 90 }, | 90 }, |
| 91 } | 91 } |
| 92 listtracks = trackList | 92 listtracks = trackList |
| 93 # foo.paf must have a foo_paf.fasta or fasta.gz to match | |
| 94 tnames = [x[2] for x in listtracks] | 93 tnames = [x[2] for x in listtracks] |
| 95 texts = [x[1] for x in listtracks] | 94 texts = [x[1] for x in listtracks] |
| 96 for i, track in enumerate(listtracks): | 95 for i, track in enumerate(listtracks): |
| 97 track_conf = { | 96 track_conf = { |
| 98 "trackfiles": [], | 97 "trackfiles": [], |
| 103 track_conf["dataset_id"] = trackname | 102 track_conf["dataset_id"] = trackname |
| 104 useuri = "no" | 103 useuri = "no" |
| 105 if tpath.startswith("http://") or tpath.startswith("https://"): | 104 if tpath.startswith("http://") or tpath.startswith("https://"): |
| 106 useuri = "yes" | 105 useuri = "yes" |
| 107 if trext == "paf": | 106 if trext == "paf": |
| 108 refname = trackname + "_paf.fasta" | 107 refdat = ["%s ~ %s" % (x[0],x[2]) for x in listtracks if x[1] in ["fasta", "fasta.gz"]] |
| 109 refdat = [x[2] for x in listtracks if x[2] == refname] | 108 if len(refdat) == 0: |
| 110 if not refdat: | |
| 111 jc.logging.warn( | 109 jc.logging.warn( |
| 112 "!! No reference file %s corresponding to paf file %s found. Not building - there must be a corresponding fasta for each paf" | 110 "!! No reference file for %s found. Using main reference" |
| 113 % (refname, trackname) | 111 % (refname) |
| 114 ) | 112 ) |
| 115 sys.exit(3) | 113 refdat = ["%s ~ %s" % (genomes[0].path, assref_name),] |
| 116 else: | 114 else: |
| 117 track_conf.update( | 115 track_conf.update( |
| 118 { | 116 { |
| 119 "conf": { | 117 "conf": { |
| 120 "options": { | 118 "options": { |
| 121 "paf": { | 119 "paf": { |
| 122 "genome": refdat, | 120 "genome": ",".join(refdat) |
| 123 "genome_label": trackname, | |
| 124 } | 121 } |
| 125 } | 122 } |
| 126 } | 123 } |
| 127 } | 124 } |
| 128 ) | 125 ) |