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galaxy.visualization.data_providers.phyloviz package¶
Data providers code for PhyloViz
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class
galaxy.visualization.data_providers.phyloviz.
PhylovizDataProvider
(original_dataset=None)[source]¶ Bases:
galaxy.visualization.data_providers.basic.BaseDataProvider
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dataset_type
= 'phylo'¶
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Submodules¶
galaxy.visualization.data_providers.phyloviz.baseparser module¶
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class
galaxy.visualization.data_providers.phyloviz.baseparser.
Node
(nodeName, **kwargs)[source]¶ Bases:
object
Node class of PhyloTree, which represents a CLAUDE in a phylogenetic tree
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class
galaxy.visualization.data_providers.phyloviz.baseparser.
PhyloTree
[source]¶ Bases:
object
Standardized python based class to represent the phylogenetic tree parsed from different phylogenetic file formats.
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addAttributesToRoot
(attrDict)[source]¶ Adds attributes to root, but first we put it in a temp store and bind it with root when .toJson is called
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galaxy.visualization.data_providers.phyloviz.newickparser module¶
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class
galaxy.visualization.data_providers.phyloviz.newickparser.
Newick_Parser
[source]¶ Bases:
galaxy.visualization.data_providers.phyloviz.baseparser.Base_Parser
For parsing trees stored in the newick format (.nhx) It is necessarily more complex because this parser is later extended by Nexus for parsing newick as well..
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parseFile
(filePath)[source]¶ Parses a newick file to obtain the string inside. Returns: jsonableDict
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parseData
(newickString)[source]¶ To be called on a newickString directly to parse it. Returns: jsonableDict
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cleanNewickString
(rawNewick)[source]¶ removing semi colon, and illegal json characters (,’,”) and white spaces
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parseNode
(string, depth)[source]¶ Recursive method for parsing newick string, works by stripping down the string into substring of newick contained with brackers, which is used to call itself.
Eg … ( A, B, (D, E)C, F, G ) …
We will make the preceeding nodes first A, B, then the internal node C, its children D, E, and finally the succeeding nodes F, G
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galaxy.visualization.data_providers.phyloviz.nexusparser module¶
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class
galaxy.visualization.data_providers.phyloviz.nexusparser.
Nexus_Parser
[source]¶ Bases:
galaxy.visualization.data_providers.phyloviz.newickparser.Newick_Parser
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parseNexus
(filename)[source]¶ Nexus data is stored in blocks between a line starting with begin and another line starting with end; Commends inside square brackets are to be ignored, For more information: http://wiki.christophchamp.com/index.php/NEXUS_file_format Nexus can store multiple trees
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galaxy.visualization.data_providers.phyloviz.phyloxmlparser module¶
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class
galaxy.visualization.data_providers.phyloviz.phyloxmlparser.
Phyloxml_Parser
[source]¶ Bases:
galaxy.visualization.data_providers.phyloviz.baseparser.Base_Parser
Parses a phyloxml file into a json file that will be passed to PhyloViz for display