def readData(filepath, format=FileFormats.NEXUS, out=None):
"""Returns a data matrix (or None if there is no data) from `filepath`
Currently only supports NEXUS and only returns the last data matrix, but
this will be generalized to read other formats and return the
supermatrix of all data matrices in the file."""
_readFileSanityCheck(filepath, format, out)
from phycas.ReadNexus import NexusReader
reader = NexusReader()
reader.readFile(filepath)
return reader.getLastDiscreteMatrix(True)
def readFileNoSideEffects(filepath, format=FileFormats.NEXUS, out=None):
"""Returns a (list of taxon labels, DataSource, TreeCollection) from the file `filepath`"""
_readFileSanityCheck(filepath, format, out)
from phycas.ReadNexus import NexusReader
reader = NexusReader()
reader.readFile(filepath)
x = PhyloPackage()
x.taxon_labels = reader.taxa
matrix = reader.getLastDiscreteMatrix(True)
x.characters = DataSource(matrix=matrix, taxon_labels=x.taxon_labels)
x.trees = TreeCollection(trees=reader.getTrees(), taxon_labels=x.taxon_labels)
return x
def readTrees(filepath, format=FileFormats.NEXUS, out=None):
"""Returns a (taxon_list, list of TreeDescription objects) (or an empty list if there are no trees) from `filepath`
Currently only supports NEXUS and only returns the last data matrix, but
this will be generalized to read other formats and return the
supermatrix of all data matrices in the file."""
_readFileSanityCheck(filepath, format, out)
from phycas.ReadNexus import NexusReader
reader = NexusReader()
reader.readFile(filepath)
return reader.taxa, reader.getTrees()