Bio.Nexus.Nexus

Package Bio :: Package Nexus :: Module Nexus

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Module Bio.Nexus.Nexus

Nexus class. Parse the contents of a nexus file. Based upon 'NEXUS: An extensible file format for systematic information' Maddison, Swofford, Maddison. 1997. Syst. Biol. 46(4):590-621

Classes
`Block`	Represent a NEXUS block with block name and list of commandlines .
`CharBuffer`	Helps reading NEXUS-words and characters from a buffer.
`Commandline`	Represent a commandline as command and options.
`Nexus`
`StepMatrix`	Calculate a stepmatrix for weighted parsimony.

Exceptions
`NexusError`

Function Summary
	`combine(matrices)` Combine matrices in [(name,nexus-instance),...] and return new nexus instance.
	`get_start_end(sequence, skiplist)` Return position of first and last character which is not in skiplist (defaults to ['-','?']).
	`quotestrip(word)` Remove quotes and/or double quotes around identifiers.
	`safename(name, mrbayes)` Return a taxon identifier according to NEXUS standard.

Function Details

combine(matrices)

Combine matrices in [(name,nexus-instance),...] and return new nexus instance.

combined_matrix=combine([(name1,nexus_instance1),(name2,nexus_instance2),...] Character sets, character partitions and taxon sets are prefixed, readjusted and present in the combined matrix.

get_start_end(sequence, skiplist=['-', '?'])

Return position of first and last character which is not in skiplist (defaults to ['-','?']).

quotestrip(word)

Remove quotes and/or double quotes around identifiers.

safename(name, mrbayes=False)

Return a taxon identifier according to NEXUS standard. Wrap quotes around names with punctuation or whitespace, and double single quotes. mrbayes=True: write names without quotes, whitespace or punctuation for mrbayes.

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