Mercurial > repos > fubar > jbrowse2
comparison jbrowse2.py @ 65:c81902830900 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 6dac6d6debf44c68eae2785e926fb8420f76958e
| author | fubar |
|---|---|
| date | Thu, 28 Mar 2024 10:31:07 +0000 |
| parents | 497fd2d27aa2 |
| children | c4eb6a85db70 |
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| 64:497fd2d27aa2 | 65:c81902830900 |
|---|---|
| 13 import tempfile | 13 import tempfile |
| 14 import urllib.request | 14 import urllib.request |
| 15 import xml.etree.ElementTree as ET | 15 import xml.etree.ElementTree as ET |
| 16 from collections import defaultdict | 16 from collections import defaultdict |
| 17 | 17 |
| 18 logging.basicConfig(level=logging.INFO) | 18 logging.basicConfig(level=logging.DEBUG) |
| 19 log = logging.getLogger("jbrowse") | 19 log = logging.getLogger("jbrowse") |
| 20 | 20 |
| 21 JB2VER = "v2.10.3" | 21 JB2VER = "v2.10.3" |
| 22 # version pinned for cloning | 22 # version pinned for cloning |
| 23 | 23 |
| 1341 "displays": [style_data], | 1341 "displays": [style_data], |
| 1342 } | 1342 } |
| 1343 ) | 1343 ) |
| 1344 # The view for the assembly we're adding | 1344 # The view for the assembly we're adding |
| 1345 view_json = {"type": "LinearGenomeView", "tracks": tracks_data} | 1345 view_json = {"type": "LinearGenomeView", "tracks": tracks_data} |
| 1346 refName = None | 1346 refName = self.assmeta[gnome][0].get("genome_firstcontig", None) |
| 1347 drdict = { | 1347 drdict = { |
| 1348 "reversed": False, | 1348 "reversed": False, |
| 1349 "assemblyName": gnome, | 1349 "assemblyName": gnome, |
| 1350 "start": 1, | 1350 "start": 1, |
| 1351 "end": 100000, | 1351 "end": 100000, |
| 1352 "refName": "x", | 1352 "refName": refName |
| 1353 } | 1353 } |
| 1354 | 1354 ddl = default_data.get("defaultLocation", None) |
| 1355 if default_data.get("defaultLocation", ""): | 1355 if ddl: |
| 1356 ddl = default_data["defaultLocation"] | |
| 1357 loc_match = re.search(r"^([^:]+):([\d,]*)\.*([\d,]*)$", ddl) | 1356 loc_match = re.search(r"^([^:]+):([\d,]*)\.*([\d,]*)$", ddl) |
| 1358 # allow commas like 100,000 but ignore as integer | 1357 # allow commas like 100,000 but ignore as integer |
| 1359 if loc_match: | 1358 if loc_match: |
| 1360 refName = loc_match.group(1) | 1359 refName = loc_match.group(1) |
| 1361 drdict["refName"] = refName | 1360 drdict["refName"] = refName |
| 1366 else: | 1365 else: |
| 1367 logging.info( | 1366 logging.info( |
| 1368 "@@@ regexp could not match contig:start..end in the supplied location %s - please fix" | 1367 "@@@ regexp could not match contig:start..end in the supplied location %s - please fix" |
| 1369 % ddl | 1368 % ddl |
| 1370 ) | 1369 ) |
| 1371 else: | |
| 1372 drdict["refName"] = gnome | |
| 1373 if drdict.get("refName", None): | 1370 if drdict.get("refName", None): |
| 1374 # TODO displayedRegions is not just zooming to the region, it hides the rest of the chromosome | 1371 # TODO displayedRegions is not just zooming to the region, it hides the rest of the chromosome |
| 1375 view_json["displayedRegions"] = [ | 1372 view_json["displayedRegions"] = [ |
| 1376 drdict, | 1373 drdict, |
| 1377 ] | 1374 ] |