I'm having a problem displaying NEXUS files in Galaxy's Phyloviz viewer. Any help would be greatly appreciated. When I try and view the simple nexus file I get the error below:
Error Traceback:
View as: Interactive | Text | XML (full)
⇝ IndexError: list index out of range
URL: http://10.20.52.124:8080/visualization/phyloviz?dataset_id=51af33325a250fc7
Module weberror.evalexception.middleware:364 in respond
view
>> app_iter = self.application(environ, detect_start_response)
Module paste.recursive:84 in __call__
view
>> return self.application(environ, start_response)
Module paste.httpexceptions:633 in __call__
view
>> return self.application(environ, start_response)
Module galaxy.web.framework.base:132 in __call__
view
>> return self.handle_request( environ, start_response )
Module galaxy.web.framework.base:190 in handle_request
view
>> body = method( trans, **kwargs )
Module galaxy.webapps.galaxy.controllers.visualization:1010 in phyloviz
view
>> data = pd.get_data( tree_index=tree_index )
Module galaxy.visualization.data_providers.phyloviz:36 in get_data
view
>> jsonDicts, parseMsg = nexusParser.parseFile( file_name )
Module galaxy.visualization.data_providers.phyloviz.nexusparser:15 in parseFile
view
>> return self.parseNexus(filePath)
Module galaxy.visualization.data_providers.phyloviz.nexusparser:65 in parseNexus
view
>> key, value = mappingLine[1], mappingLine[2].replace(",", "").replace("'","") #replacing illegal json characters
IndexError: list index out of range
Nexus File:
#NEXUS
[R-package APE, Mon Oct 27 17:31:54 2014]
BEGIN TAXA;
DIMENSIONS NTAX = 4;
TAXLABELS
GCA_000003215
GCA_000027105
GCA_000450925
GCA_000449745
;
END;
BEGIN TREES;
TRANSLATE
1 GCA_000003215,
2 GCA_000027105,
3 GCA_000450925,
4 GCA_000449745
;
TREE * UNTITLED = [&U] (4:0.0001390332429,3:9.926730628e-05,(1:1.873724177e-05,2:3.650049072e-06):0.008631185479);
END;