Trees | Indices | Help |
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PhyloXML reader/parser, writer, and associated functions.
Instantiates tree elements from a parsed PhyloXML file, and constructs an XML file from a Bio.Phylo.PhyloXML object.
About capitalization:
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PhyloXMLError Exception raised when PhyloXML object construction cannot continue. |
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Parser Methods for parsing all phyloXML nodes from an XML stream. |
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Writer Methods for serializing a PhyloXML object to XML. |
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NAMESPACES =
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__package__ =
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prefix =
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uri =
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Parse a phyloXML file or stream and build a tree of Biopython objects. The children of the root node are phylogenies and possibly other arbitrary (non-phyloXML) objects.
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Iterate over the phylogenetic trees in a phyloXML file. This ignores any additional data stored at the top level, but may be more memory-efficient than the read function.
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Find a child node by tag, and pass it through a constructor. Returns None if no matching child is found. |
Find a child node by tag; pass its text through a constructor. Returns None if no matching child is found. |
Find child nodes by tag; pass each through a constructor. Returns an empty list if no matching child is found. |
Find child nodes by tag; pass each node's text through a constructor. Returns an empty list if no matching child is found. |
Add line breaks and indentation to ElementTree in-place. Sources:
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Replace all spans of whitespace with a single space character. Also remove leading and trailing whitespace. See "Collapse Whitespace Policy" in the phyloXML spec glossary: http://phyloxml.org/documentation/version_100/phyloxml.xsd.html#Glossary |
Replace tab, LF and CR characters with spaces, but don't collapse. See "Replace Whitespace Policy" in the phyloXML spec glossary: http://phyloxml.org/documentation/version_100/phyloxml.xsd.html#Glossary |
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NAMESPACES
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