B b\ @sHdZddlmZddlmZddlmZmZdZdZ ddZ d d Z d S) z.I/O function wrappers for ``Bio.Nexus`` trees.)chain)Nexus)NewickNewickIOzh#NEXUS Begin Taxa; Dimensions NTax=%(count)d; TaxLabels %(labels)s; End; Begin Trees; %(trees)s End; zTree tree%(index)d=%(tree)sc#sVt|}fddx:|jD]0}|||j}tj||j|j|jdVqWdS)aUParse the trees in a Nexus file. Uses the old Nexus.Trees parser to extract the trees, converts them back to plain Newick trees, and feeds those strings through the new Newick parser. This way we don't have to modify the Nexus module yet. (Perhaps we'll eventually change Nexus to use the new NewickIO parser directly.) cs:fdd|jD}tj|jj|jj||jj|jjdS)Ncsg|]}|qS)node).0n) node2cladenxtreer0lib/python3.7/site-packages/Bio/Phylo/NexusIO.py .sz-parse..node2clade..)Z branch_lengthnameZcladesZ confidencecomment)ZsuccrZCladedataZ branchlengthZtaxonZsupportr)r rZ subclades)r )r r r -szparse..node2clade)rootrootedrweightN) rtreesrrrZTreerrr)handleZnexr Znewrootr)r r parse s   rcKst|}t|}ddt|jfddd|D}ddtdd|DD}tt|d |d |d }| |t|S) zWrite a new Nexus file containing the given trees. Uses a simple Nexus template and the NewickIO writer to serialize just the trees and minimal supporting info needed for a valid Nexus file. cSs"g|]\}}t|d|dqS))indexZtree) TREE_TEMPLATE)ridxZnwkrrr r Gszwrite..FT)ZplainZ plain_newickcSsg|]}t|jqSr)strr)rxrrr r Lscss|]}|VqdS)N)Z get_terminals)rtrrr Lszwrite..  )countlabelsr) listrWriter enumerateZ to_stringsr NEX_TEMPLATElenjoinwrite)objrkwargsrwriterZ nexus_treesZ tax_labelstextrrr r)>s  r)N) __doc__ itertoolsrZ Bio.NexusrZ Bio.Phylorrr&rrr)rrrr s