Package Bio :: Package Nexus :: Module Nexus
[show private | hide private]
[frames | no frames]

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.

Generated by Epydoc 2.1 on Mon Aug 27 16:13:13 2007 http://epydoc.sf.net