{Tip LdZddlmZddlmZddlmZddlmZdZdZ dZ d Z y ) z.I/O function wrappers for ``Bio.Nexus`` trees.)chain)Nexus)Newick)NewickIOzh#NEXUS Begin Taxa; Dimensions NTax=%(count)d; TaxLabels %(labels)s; End; Begin Trees; %(trees)s End; zTree tree%(index)d=%(tree)sc#Ktj|}fd|jD]]}||j|j}t j ||j |j|j_yw)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.) c @|jDcgc]}||j|}}tj|jj |jj ||jj|jjScc}w)N) branch_lengthnameclades confidencecomment) succnoderCladedata branchlengthtaxonsupportr )nxtreern subclades node2clades D/home/agent/.local/lib/python3.12/site-packages/Bio/Phylo/NexusIO.pyrzparse..node2clade-suAEKAZ A7K K||))00yy((II%%   LsB)rootrootedr weightN) rtreesrrrTreerr r)handlenexrnewrootrs @rparser" sp ++f C  )) VV[[%=>kkV[[   sBB c t|}tj|}t|jd ddd|Dcgc]\}}t |dz|dz}}}t d|DDcgc]}t|j} }tt| dj| dj|d z} |j| t|Scc}}wcc}w) 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. FT)plain plain_newick)indextreec3<K|]}|jyw)N) get_terminals).0ts r zwrite..Ls.PQq/@.Ps  )countlabelsr) listrWriter enumerate to_strings TREE_TEMPLATErstrr NEX_TEMPLATElenjoinwrite) objrkwargsrwriteridxnwk nexus_treesx tax_labelstexts rr<r<>s IE __U #F" F   GE G G  C #'377K (-.P%.P'QR!#aff+RJR Z((:&;' D  LL {  Ss C/C#N) __doc__ itertoolsr Bio.Nexusr Bio.Phylorrr9r7r"r<r2rrKs.5  .  <rJ