o Rŀg^@sdZddlZddlZddlmZddlmZddlmZGddde Z dd Z d$d d Z d d Z ddZddZddZd%ddZddZddZddZddZddZd d!Zd"d#ZdS)&zClasses and methods for finding consensus trees. This module contains a ``_BitString`` class to assist the consensus tree searching and some common consensus algorithms such as strict, majority rule and adam consensus. N) literal_eval)MultipleSeqAlignment)BaseTreec@seZdZdZddZddZddZdd Zd d Zd d Z ddZ ddZ ddZ ddZ ddZddZddZeddZdS) _BitStringaFHelper class for binary string data (PRIVATE). Assistant class of binary string data used for storing and counting compatible clades in consensus tree searching. It includes some binary manipulation(&|^~) methods. _BitString is a sub-class of ``str`` object that only accepts two characters('0' and '1'), with additional functions for binary-like manipulation(&|^~). It is used to count and store the clades in multiple trees in consensus tree searching. During counting, the clades will be considered the same if their terminals(in terms of ``name`` attribute) are the same. For example, let's say two trees are provided as below to search their strict consensus tree:: tree1: (((A, B), C),(D, E)) tree2: ((A, (B, C)),(D, E)) For both trees, a _BitString object '11111' will represent their root clade. Each '1' stands for the terminal clade in the list [A, B, C, D, E](the order might not be the same, it's determined by the ``get_terminal`` method of the first tree provided). For the clade ((A, B), C) in tree1 and (A, (B, C)) in tree2, they both can be represented by '11100'. Similarly, '11000' represents clade (A, B) in tree1, '01100' represents clade (B, C) in tree2, and '00011' represents clade (D, E) in both trees. So, with the ``_count_clades`` function in this module, finally we can get the clade counts and their _BitString representation as follows (the root and terminals are omitted):: clade _BitString count ABC '11100' 2 DE '00011' 2 AB '11000' 1 BC '01100' 1 To get the _BitString representation of a clade, we can use the following code snippet:: # suppose we are provided with a tree list, the first thing to do is # to get all the terminal names in the first tree term_names = [term.name for term in trees[0].get_terminals()] # for a specific clade in any of the tree, also get its terminal names clade_term_names = [term.name for term in clade.get_terminals()] # then create a boolean list boolvals = [name in clade_term_names for name in term_names] # create the string version and pass it to _BitString bitstr = _BitString(''.join(map(str, map(int, boolvals)))) # or, equivalently: bitstr = _BitString.from_bool(boolvals) To convert back:: # get all the terminal clades of the first tree terms = [term for term in trees[0].get_terminals()] # get the index of terminal clades in bitstr index_list = bitstr.index_one() # get all terminal clades by index clade_terms = [terms[i] for i in index_list] # create a new calde and append all the terminal clades new_clade = BaseTree.Clade() new_clade.clades.extend(clade_terms) Examples -------- >>> from Bio.Phylo.Consensus import _BitString >>> bitstr1 = _BitString('11111') >>> bitstr2 = _BitString('11100') >>> bitstr3 = _BitString('01101') >>> bitstr1 _BitString('11111') >>> bitstr2 & bitstr3 _BitString('01100') >>> bitstr2 | bitstr3 _BitString('11101') >>> bitstr2 ^ bitstr3 _BitString('10001') >>> bitstr2.index_one() [0, 1, 2] >>> bitstr3.index_one() [1, 2, 4] >>> bitstr3.index_zero() [0, 3] >>> bitstr1.contains(bitstr2) True >>> bitstr2.contains(bitstr3) False >>> bitstr2.independent(bitstr3) False >>> bitstr1.iscompatible(bitstr2) True >>> bitstr2.iscompatible(bitstr3) False cCs:t|trt||d|dkrt||Std)zInit from a binary string data.01z;The input should be a binary string composed of '0' and '1') isinstancestrlencount__new__ TypeError)clsstrdatarG/var/www/html/myenv/lib/python3.10/site-packages/Bio/Phylo/Consensus.pyr zs z_BitString.__new__cCs>td|}td|}||@}tt|ddt|SN0brrbinzfillr selfotherselfintotherint resultintrrr__and__  z_BitString.__and__cCs>td|}td|}||B}tt|ddt|Srrrrrr__or__rz_BitString.__or__cCs>td|}td|}||A}tt|ddt|Srrrrrr__xor__rz_BitString.__xor__cCs>td|}td|}||@}tt|ddt|Srrrrrr__rand__rz_BitString.__rand__cCs>td|}td|}||B}tt|ddt|Srrrrrr__ror__rz_BitString.__ror__cCs>td|}td|}||A}tt|ddt|Srrrrrr__rxor__rz_BitString.__rxor__cCsdt|dS)Nz _BitString())r __repr__rrrrr&sz_BitString.__repr__cCddt|DS)z4Return a list of positions where the element is '1'.cSg|] \}}|dkr|qS)rr.0inrrr z(_BitString.index_one.. enumerater'rrr index_onez_BitString.index_onecCr()z4Return a list of positions where the element is '0'.cSr))rrr*rrrr.r/z)_BitString.index_zero..r0r'rrr index_zeror3z_BitString.index_zerocCs&||A}|d|d|dkS)azCheck if current bitstr1 contains another one bitstr2. That is to say, the bitstr2.index_one() is a subset of bitstr1.index_one(). Examples: "011011" contains "011000", "011001", "000011" Be careful, "011011" also contains "000000". Actually, all _BitString objects contain all-zero _BitString of the same length. rr rrxorbitrrrcontainss z_BitString.containscCs&||A}|d|d|dkS)aCheck if current bitstr1 is independent of another one bitstr2. That is to say the bitstr1.index_one() and bitstr2.index_one() have no intersection. Be careful, all _BitString objects are independent of all-zero _BitString of the same length. rr5r6rrr independents z_BitString.independentcCs||p||p||S)zCheck if current bitstr1 is compatible with another bitstr2. Two conditions are considered as compatible: 1. bitstr1.contain(bitstr2) or vice versa; 2. bitstr1.independent(bitstr2). )r8r9)rrrrr iscompatiblesz_BitString.iscompatiblecCs|dtttt|S)N)joinmapr int)rboolsrrr from_boolsz_BitString.from_boolN)__name__ __module__ __qualname____doc__r rr r!r"r#r$r&r2r4r8r9r: classmethodr@rrrrrs"b   rc s>t|}t|}|tt|g|\}fdd|D}|jddddt }|d dt krA|j ntd |d|i}|d d D]G}fd d|Dt }|j |D]'\} } | |r|| =fd d| j D| _ | j || |A} | || <nql|||<qQtj|dS)zSearch strict consensus tree from multiple trees. :Parameters: trees : iterable iterable of trees to produce consensus tree. cs g|] \}}|dkr|qSrr)r+bitstrt) tree_countrrr.sz$strict_consensus..cS |dSNrr5rGrrr z"strict_consensus..Tkeyreverserr-Taxons in provided trees should be consistentNcg|]}|qSrrr+r,termsrrr.cg|]}|vr|qSrr)r+child clade_termsrrr.root)iternext get_terminals _count_clades itertoolschainitemssortrClader r cladesextend ValueErrorr2r8appendTree) trees trees_iter first_tree bitstr_countsstrict_bitstrsr_ bitstr_cladesrGcladebscr)r\rWrIrstrict_consensuss8      rwcsrt|}t|}|tt|g|\}tfdddd}t }|d dt kr:|j ntd|d|i}|dd D]}|\} } d | |} | |d kr`nӇfd d |Dt } | j | | _| | | _t|d ddd} d}d }g}| D]+|sd}n!|r}|r|krtfdd|Dr|q|sqJ|r||}fdd |j D|_ |j | |||<|rg}|D]}| |||}|j || j |qfdd |Dfdd | j D| _ | ||<t |t dks0t |t dkr2t |j dkr2nqJtj|dS)a7Search majority rule consensus tree from multiple trees. This is a extend majority rule method, which means the you can set any cutoff between 0 ~ 1 instead of 0.5. The default value of cutoff is 0 to create a relaxed binary consensus tree in any condition (as long as one of the provided trees is a binary tree). The branch length of each consensus clade in the result consensus tree is the average length of all counts for that clade. :Parameters: trees : iterable iterable of trees to produce consensus tree. cs|d|dt|fS)Nrr)r r rL)rqrrrM*r/z$majority_consensus..TrOrrrRrSNY@crTrrrUrVrrr.;rXz&majority_consensus..cSrJrKr5rurrrrM@rNFc3s|]}|VqdSN)r9r+rvryrr Tsz%majority_consensus..crYrrr{r[rrr.^scrTrrrUrVrrr.orXcrYrrr{) remove_termsrrr.pr]rr^)r`rarbrcrdresortedkeysrrhr r rirjrkr2 confidence branch_lengthr:r8allrlpopremoverm)rncutoff tree_iterrprIbitstrsr_rsrGcount_in_treesbranch_length_sumrrtbsckeys compatible parent_bitstr child_bitstrs parent_clade remove_listrv child_clader)rqrur\r}rWrmajority_consensuss              & rcCs dd|D}tjt|ddS)zSearch Adam Consensus tree from multiple trees. :Parameters: trees : list list of trees to produce consensus tree. cSg|]}|jqSrr^)r+treerrrr.z"adam_consensus..T)r_rooted)rrm_part)rnrirrradam_consensuszsrcsPd}|d}dd|Dt|dkst|dkr!|d}|Stdt|h}|D]}|jD]}t|}t}t}|D]N} | |krGq@| |r^|||| |A|| q@|| rk|| |Aq@| |s|| |@|| |@|A|| |@| A|| q@||N}|rt |dd d D]} d } |D] } | | sd } nq| r|| qq1q,t }t |D]d}| } t| dkr|j || dqt| dkrt } | j || d| j || d|j | qt| dkr%fd d| D}g}|D] }| t||q|j t|q|S)z:Recursive function for Adam Consensus algorithm (PRIVATE).NrcSrrnamer+termrrrr.rz_part..rSrrcSrJrKr5ryrrrrMrNz_part..)rPTFcrTrrrU term_namesrrr.rX)rbr rri_clade_to_bitstrsetr8addr9rrrhr2rl _sub_clader)ri new_claderWrrtrZrG to_removeto_addrutar9indices bifur_clade part_names next_cladesrrrrst 2             rc sfdd|D}|}t||krqt}|j||jdddD]G}||jkr/q't |jddt |@}|rn|jdddD])}t |j}||} | |rm| rmt | |_t} | jt ||j | qDq'|}|S)zTExtract a compatible subclade that only contains the given terminal names (PRIVATE).csg|]}|qSr)find_anyr+rrtrrr.sz_sub_clade..Fpreorder)terminalorderTr) common_ancestorr count_terminalsrrhrirj find_cladesr_rissubsetlistrl) rtr term_clades sub_clade temp_cladervchildrentc tc_children tc_new_cladesrrrrrs*      rc Csi}d}|D]<}|d7}t|}|jddD]+}||}||vr8||\}}|d7}||jp/d7}||f||<qd|jp=df||<qq||fS)awCount distinct clades (different sets of terminal names) in the trees (PRIVATE). Return a tuple first a dict of bitstring (representing clade) and a tuple of its count of occurrences and sum of branch length for that clade, second the number of trees processed. :Parameters: trees : iterable An iterable that returns the trees to count rrSFr)_tree_to_bitstrsrr) rnrrIr clade_bitstrsrtrGr sum_blrrrrcs   rcc Cstdd|jddD}i}|}|dur(zt|}Wn ty'tddw|jddD] }t||}|df||<q.|D]+}|jddD]"}t||}||vrh||\} } | d d || _| | d f||<qFq>|S) aCalculate branch support for a target tree given bootstrap replicate trees. :Parameters: target_tree : Tree tree to calculate branch support for. trees : iterable iterable of trees used to calculate branch support. len_trees : int optional count of replicates in trees. len_trees must be provided when len(trees) is not a valid operation. css|]}|jVqdSrzrrrrrr|szget_support..TrNzzTrees does not support len(trees), you must provide the number of replicates in trees as the optional parameter len_trees.FrrSrx)rrr r rr) target_treern len_treesrrsizertrGrrvrHrrr get_supports4      rccst|d}d}||krH|d7}d}t|D]'}td|d}|s0|dd||df}q||dd||df7}q|V||ks dSdS)aGenerate bootstrap replicates from a multiple sequence alignment (OBSOLETE). :Parameters: msa : MultipleSeqAlignment multiple sequence alignment to generate replicates. times : int number of bootstrap times. rrSN)r rangerandomrandint)msatimeslengthr,itemjcolrrr bootstraps  rc #st|trMt|d}t|D]:}d}t|D])}td|d}|dur3|dd||df}q||dd||df7}q||}|VqdS|j\} t|D]}fddtD} ||dd| f}|VqVdS)ayGenerate bootstrap replicate trees from a multiple sequence alignment. :Parameters: alignment : Alignment or MultipleSeqAlignment object multiple sequence alignment to generate replicates. times : int number of bootstrap times. tree_constructor : TreeConstructor tree constructor to be used to build trees. rNrScsg|] }tddqS)rrS)rr)r+rmrrr.Pr/z#bootstrap_trees..)rrr rrr build_treeshape) alignmentrtree_constructorrr,bootstrapped_alignmentrrrr-colsrrrbootstrap_trees5s&     rcCst|||}||}|S)aConsensus tree of a series of bootstrap trees for a multiple sequence alignment. :Parameters: alignment : Alignment or MultipleSeqAlignment object Multiple sequence alignment to generate replicates. times : int Number of bootstrap times. tree_constructor : TreeConstructor Tree constructor to be used to build trees. consensus : function Consensus method in this module: ``strict_consensus``, ``majority_consensus``, ``adam_consensus``. )r)rrr consensusrnrrrrbootstrap_consensusUs rcs.dd|jddDtfdd|DS)zRCreate a BitString representing a clade, given ordered tree taxon names (PRIVATE).cSh|]}|jqSrrrrrr krz#_clade_to_bitstr..Trc3s|]}|vVqdSrzrrclade_term_namesrrr|lsz#_clade_to_bitstr..)rrr@)rttree_term_namesrrrrisrcCsBi}dd|jddD}|jddD] }t||}|||<q|S)zGCreate a dict of a tree's clades to corresponding BitStrings (PRIVATE).cSrrrrrrrr.rrz$_tree_to_bitstrs..TrF)rr)rclades_bitstrsrrtrGrrrros   rcCs2i}t|D]\}}t|jpdd||<q|S)zGenerate a branch length dict for a tree, keyed by BitStrings (PRIVATE). Create a dict of all clades' BitStrings to the corresponding branch lengths (rounded to 5 decimal places). g)rrfroundr)rrrtrGrrr_bitstring_topologyysrcCsDdd|jddD}dd|jddD}||ko!t|t|kS)zAre two trees are equal in terms of topology and branch lengths (PRIVATE). (Branch lengths checked to 5 decimal places.) cSrrrrrrrrrz"_equal_topology..TrcSrrrrrrrrr)rr)tree1tree2 term_names1 term_names2rrr_equal_topologys rrFrz)rDrdrastr Bio.Alignr Bio.Phylorr rrwrrrrrcrrrrrrrrrrrrs,   I 3h ; (