https://github.com/blab/mumps-wa-phylodynamics
Tip revision: b8358a0d49d70670dbab9eeffa9972c277b3021b authored by Louise Moncla on 17 March 2021, 19:25:20 UTC
adding in callouts for Wisconsin H and A genomes
adding in callouts for Wisconsin H and A genomes
Tip revision: b8358a0
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e e e d Z e d k rld d l Z e e j d e Z e j e j j d e j n d S( iÿÿÿÿNs %Y-%m-%dt -c C sæ | t k rz t | j | } | d k rL | j | j | d } qz | d k rz | j | j | d } qz n t j j | | } | j } t j | d d } t j | d d d } | | | j | | j S( s> Converts calendar dates in specified format to decimal date. i iÿÿÿÿi iþÿÿÿ( t Truet lent splitt joint dtt datetimet strptimet yeart
total_seconds( t datet fmtt variablet dateSplittert dateLt adatetimeR t boyt eoy( ( s# /Users/lmoncla/src/baltic/baltic.pyt decimalDate s " c C s" t j j t j j | | | S( s/ Converts calendar dates between given formats ( R R t strftimeR ( t xt startt end( ( s# /Users/lmoncla/src/baltic/baltic.pyt convertDate s t cladec B s e Z d Z RS( c C s d | _ d | _ d | _ d | _ d | _ d | _ d | _ i | _ d | _ | | _
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d | _ d | _ d | _ d S( Nt leafg i ( t
branchTypet Nonet subtreet leavest lengtht heightt absoluteTimet parentt traitst indext namet numNameR t yt
lastHeightt lastAbsoluteTimet width( t selft givenName( ( s# /Users/lmoncla/src/baltic/baltic.pyt __init__ s ( t __name__t
__module__R, ( ( ( s# /Users/lmoncla/src/baltic/baltic.pyR s t nodec B s e Z d Z RS( c C ss d | _ d | _ d | _ d | _ d | _ g | _ i | _ d | _ d | _ d | _
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d S( NR/ g ( R R R R R R! t childrenR" R# t childHeightR R& t setR ( R* ( ( s# /Users/lmoncla/src/baltic/baltic.pyR, . s ( R- R. R, ( ( ( s# /Users/lmoncla/src/baltic/baltic.pyR/ - s R c B s e Z d Z RS( c C sg d | _ d | _ d | _ d | _ d | _ d | _ d | _ d | _ i | _ d | _
d | _ d S( NR ( R R R$ R% R# R R R R! R" R R& ( R* ( ( s# /Users/lmoncla/src/baltic/baltic.pyR, > s ( R- R. R, ( ( ( s# /Users/lmoncla/src/baltic/baltic.pyR = s t treec B sÐ e Z d Z d Z d Z d2 d2 d Z d Z d Z d Z d2 d d d2 e
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d S( Nt Rootg i ( R/ t cur_nodeR# R R R t roott Objectst tipMapt
treeHeightt ySpan( R* ( ( s# /Users/lmoncla/src/baltic/baltic.pyR, L s c C sl t } | | _ | j d k r- | | _ n | j | _ | j j j | | | _ | j j | j d S( s& Attaches a new node to current node. N( R/ R# R6 R R5 R! R0 t appendR7 ( R* t it new_node( ( s# /Users/lmoncla/src/baltic/baltic.pyt add_nodeW s c C su t } | | _ | j d k r- | | _ n | j | _ | j j j | | | _ | | _ | j j | j d S( s* Attach a new leaf (tip) to current node. N(
R R# R6 R R5 R! R0 R; R% R7 ( R* R< R$ t new_leaf( ( s# /Users/lmoncla/src/baltic/baltic.pyt add_leafc s c sò t j | j | d d d | } | d k sg t g | D] } | j d k r= | ^ q= d k rk d St } | | _ | d | _ t | | d k rê x8 | j
D]* } t t f d | j
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q¯ W| j n | Sd S( s× Generate a subtree (as a baltic tree object) from a traversal.
k is the starting branch for traversal (default: root).
traverse_condition is a function that determines whether a child branch should be visited (default: always true).
Returns a new baltic tree instance.
Note - custom traversal functions can result in multitype trees.
If this is undesired call singleType() on the resulting subtree afterwards. t include_conditionc S s t S( N( R ( t k( ( s# /Users/lmoncla/src/baltic/baltic.pyt <lambda>w s t traverse_conditionR i c s
| k S( N( ( RB ( t subtree_set( s# /Users/lmoncla/src/baltic/baltic.pyRC s N( t copyt deepcopyt
traverse_treeR R R R3 R7 R6 R2 t getInternalt listt filterR0 t fixHangingNodes( R* RB RD R t
local_treet nd( ( RE s# /Users/lmoncla/src/baltic/baltic.pyR p s '@
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c C sM g | j D]0 } | j d k r
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} xü t | d k r>g | j D]0 } | j d k r_ t | j d k r_ | ^ q_ } x£ t | d d D] } | j d } | j } | | _ | j j | | j j | t t | j | _ | j
| j
7_
| j | | j j | q« WqC W| j d S( s= Removes any branches with a single child (multitype nodes). R/ i i t keyc S s | j S( N( R ( R ( ( s# /Users/lmoncla/src/baltic/baltic.pyRC s N( R7 R R R0 t sortedR! R; t removeRJ R2 R t sortBranches( R* RB t multiTypeNodest childt grandparent( ( s# /Users/lmoncla/src/baltic/baltic.pyt
singleType s @@
c C s/ x( | j D] } | | j | j | _ q
Wd S( sQ place all objects in absolute time by providing the date of the most recent tip N( R7 R9 R R ( R* R
R< ( ( s# /Users/lmoncla/src/baltic/baltic.pyt setAbsoluteTime s c C s | j | j } d | j t g | D] } | j ^ q& f GH| j } t } t } t } g | D] } t | j ^ qf } t | d k r t } nO t
| t | } } | d k rÖ | d k rÖ t } n | d k rë t } n t }
t g | D] } t | j ^ qû } | d k r.t }
n | r<d GHn | rJd GHn | rXd GHn |
rfd GHn d t | t | t | t | f GHd
S( s$ provide information about the tree s$
Tree height: %.6f
Tree length: %.6fi i i s strictly bifurcating trees multitype trees singleton trees annotations presents9
Numbers of objects in tree: %d (%d nodes and %d leaves)
N(
RH R7 R9 t sumR RI t FalseR R0 R t mint maxR" ( R* t obsR t nodest strictlyBifurcatingt multiTypet singletont
N_childrent minChildrent maxChildrent hasTraitst maxAnnotations( ( s# /Users/lmoncla/src/baltic/baltic.pyt treeStats£ s8
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| j d k S( NR ( R ( RB ( ( s# /Users/lmoncla/src/baltic/baltic.pyRC È s c C s t S( N( R ( RB ( ( s# /Users/lmoncla/src/baltic/baltic.pyRC È s c C sh | d k rp xA | j D]6 } | j d k rC t | _ d | _ n d | _ q W| t k rd d GHn | j } n | d k r
g } n | j r¶ | j d k r¶ | j
| j j | _ n | j d k rÑ d | _ n | t k rõ d | j | j f GHn | | r| j | n | j d k r9| j j j
| j n+| j d k rdxx t | | j D]d } | t k r|d | j GHn | j d | d | d | d
| d | | t k r[d | j GHq[q[Wt | j d
k sët d | j t g | j D]' } | j d k r| j n | j ^ qø | _ | j rU| j j j | j | j _ n | j | _ n | S( NR/ s Initiated traversal from rootg s
at %s (%s)R s visiting child %sR5 RA RD t verboset collects
child %s donei sA Tried traversing through hanging node without children. Index: %s( R R7 R R2 R R1 R R R6 R! R R# R; t addR% RK R0 RH R t AssertionErrorR[ t unionR9 ( R* R5 RA RD Rh Rg RB RT ( ( s# /Users/lmoncla/src/baltic/baltic.pyRH È sD
( (@ !c C sR | d k r' | j d k r' | j } n x$ | j D] } | | j | _ q4 Wd S( s5 Give each tip its correct label using a dictionary. N( R R8 t getExternalR% R$ ( R* t dRB ( ( s# /Users/lmoncla/src/baltic/baltic.pyt
renameTipsó s c s | t k r d n | t k r* d n xÌ | j D]¾ } t g | j D] } | j d k rJ | ^ qJ d f d } t g | j D] } | j d k r | ^ q d f d } d k rÙ | | | _ q7 d k r7 | | | _ q7 q7 W| j d S( s Sort descendants of each node. iÿÿÿÿi R/ RO c s t | j | j f S( N( R R R ( t q( t modifier( s# /Users/lmoncla/src/baltic/baltic.pyRC s R c s | j S( N( R ( Ro ( Rp ( s# /Users/lmoncla/src/baltic/baltic.pyRC s N( R RY RI RP R0 R t drawTree( R* t
descendingRB R R] R ( ( Rp s# /Users/lmoncla/src/baltic/baltic.pyRR ú s @@ c sÿ | d k r/ | j } | t k rC d GHqC n | t k rC d GHn g | D] } | j ^ qJ } g | D]( } t | t r d n
| j d ^ qf } x# | j D] } d | _ d | _ q Wd } i x2t
t
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GHn x¹t f d | j D]} | j d k r9| t k rNd | j
GHn | j } | j
| j } t | | } | t k rd | GHn t | t rÝ| | d k rÝ| | | d
8} | t k rÝd | GHqÝn | | _ | | _ d | j
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k rt | j n | j ^ qh } t | d |
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} t | | _ qÉ Wd S( s* Find x and y coordinates of each branch. s Drawing tree in pre-orders Drawing tree with provided orderi i s Drawing iteration %dc s
| j k S( N( R# ( t w( t drawn( s# /Users/lmoncla/src/baltic/baltic.pyRC " s R s Setting leaf %s y coordinate tos %sg @s adjusting clade y position to %st yRangeR/ s Setting node %s coordinatess/ Got stuck trying to find y positions of objectsN( R RH R R% t
isinstanceR R) R7 R R& R RK R R# R RX R t hasattrR! RY t setattrR0 t floatRZ Ru R[ Rj R: ( R* t orderRg R t
name_ordert skipsRB t storePlottedt y_idxR& Ro t children_y_coordsRT t minYranget maxYrange( ( Rt s# /Users/lmoncla/src/baltic/baltic.pyRq sd 5
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CC c C s | d k r t g | j D]( } t | t r7 d n
| j d ^ q } | j } x3 | j D]% } d | j d <d | _ d | _
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d t | } n$ d t j
t | j t | } | j j d k r
d | j _ d | j _
n | j j | j t j | j d | d | _ | j j
| j t j | j d | d | _
| j d } | j d k rx | j D]~ } | j d k rÇd t j
d t | } n$ d t j
t | j t | } | | j d <| | 7} | j | | qWn d S(
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Calculate x and y coordinates in an unrooted arrangement.
Code translated from https://github.com/nextstrain/auspice/commit/fc50bbf5e1d09908be2209450c6c3264f298e98c, written by Richard Neher.
i g t tauR i g ð?g à?R/ N( R RX Rl Rv R R) R6 R7 R" R R& R t matht piRy R R R! R t cost sinR0 t drawUnrooted( R* t nt totalR RB Rs t etat ch( ( s# /Users/lmoncla/src/baltic/baltic.pyR G s0 A
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c C sé g | D] } | j ^ q } t t | d k s@ t d | t k r¸ t g | D]: } | g | j D] } | j ^ ql k r d n d ^ qV t | k s!t d | ni t g | D]: } | g | j D] } | j ^ qØ k rö d n d ^ q t | k s!t d | t t | d } t
g | j D]E } | j d k sht
| t rDt | j t | k rD| ^ qDd d } | t k rg | D]] } t g | D]2 }
g | j D] } | j | ^ qÎj |
^ q¾ t | k r®| ^ q®d } ng g | D]V } t g | D]+ }
g | j D] } | ^ q?j |
^ q/ t | k r | ^ q d } | t k r| S| t k rºt | j t | k rº| S| t k råt | j t | k råd Sd S( Ni s7 More than one type of data detected in descendants listi s- Not all specified descendants are in tree: %sR/ RO c S s | j S( N( R ( R ( ( s# /Users/lmoncla/src/baltic/baltic.pyRC s s iÿÿÿÿ( t __class__R R2 Rj RY RX Rl R$ R% RJ RP R7 R Rv R R R8 t countR R ( R* t descendantsR% t strictt desct typesRB Rs t dtypet allAncestorst lt ancestor( ( s# /Users/lmoncla/src/baltic/baltic.pyt commonAncestork s $ lid qg ''c C s
t | j S( N( R R ( RB ( ( s# /Users/lmoncla/src/baltic/baltic.pyRC s c
C s | j d k s t d t | } | j | _ | j | _ | j | _ | j | _ | j | _ | j | _ | j | _ | | | _
| t k r± d | j | j j f GHn | j } | j | d d } | | _
t | t | j k st d t g | D] } | j ^ q | _ g | D] } | j ^ q.j d t | k rt g | D] } | j ^ qb | _ n x | D] } | j j | qW| j j | | j j | | j j | | | _ | j d k rù| | j | <n | j | j d S( s1 Collapse an entire subtree into a clade object. R/ s Cannot collapse non-node classs0 Replacing node %s (parent %s) with a clade classRA c S s t S( N( R ( RB ( ( s# /Users/lmoncla/src/baltic/baltic.pyRC s s! Attempted collapse of entire treeN( R Rj R R# R R R R! R R" R) R RH R R R7 R[ R' R R R( RQ R0 R; R8 RR (
R* t clR+ Rg t
widthFunctiont collapsedCladeR! t remove_from_treeR RB ( ( s# /Users/lmoncla/src/baltic/baltic.pyt collapseSubtree s: '%1(
c C s xô t g | j D] } t | t r | ^ q d k rö g | j D] } t | t rD | ^ qD } x | D] } | j } | j } | j j | | j j | d | j | 7_ | j j | | j d k rl | j j | j d ql ql Wq W| j
d S( s$ Uncollapse all collapsed subtrees. i N( R R7 Rv R R! R R0 RQ R; R8 R t popR$ RH ( R* RB t cladesR R! R ( ( s# /Users/lmoncla/src/baltic/baltic.pyt uncollapseSubtree¥ s :+
!c C s | j d d k S( Nt posteriorg à?( R" ( R ( ( s# /Users/lmoncla/src/baltic/baltic.pyRC ´ s c s© t j | t d k rH t t f d j } n g D] } | j ^ qO j d t k s
t d t g D] } | j k r | ^ q d k sÅ t d t t f d j } | t
k r d t | g | D] } | j ^ qf GHn xxt | d k r| t
k rSd t | GHn xAt | d d
D]*} | j
} | j j
| 7_
| } | j } | d k r±| j } n | t
k rñd | j g | j
D] } | j ^ qÐ| j f GHn xY j D]N } | j | k rû| | _ | j | j 7_ | t
k rId | j GHqIqûqûW| j j
j | j j | | j | t d k rº| t t f d
j k n¾ g D] } | j ^ qÁj d t k s÷t d t g D] } | j k r| ^ q d k s7t d g j D]1 } | j g D] }
|
j ^ qTk rA| ^ qA} | t
k rid | j GHqiqiWq#W j S( s Collapse all branches that satisfy a function collapseIf (default is an anonymous function that returns true if posterior probability is <=0.5).
Alternatively, a list of nodes can be supplied to the script.
Returns a deep copied version of the tree.
i c s. | j d k o- | t k o- | j k S( NR/ ( R R R6 ( R ( t
collapseIft newTree( s# /Users/lmoncla/src/baltic/baltic.pyRC » s R/ s@ Non-node class detected in list of nodes designated for deletions% Root node was designated for deletionc s# | j g D] } | j ^ q
k S( N( R# ( Rs Ro ( t designated_nodes( s# /Users/lmoncla/src/baltic/baltic.pyRC À s s %s nodes set for collapsing: %ss( Continuing collapse cycle, %s nodes leftRO c S s | j S( N( R ( R ( ( s# /Users/lmoncla/src/baltic/baltic.pyRC È s s2 Removing node %s, attaching children %s to node %ss Fixing branch length for node %sc s. | j d k o- | t k o- | j k S( NR/ ( R R R6 ( R ( R R¡ ( s# /Users/lmoncla/src/baltic/baltic.pyRC Ý s s Removing references to node %sN( RF RG R RJ RK R7 R R Rj R6 R R# RP R0 R! R R RQ RR ( R* R R¢ Rg t nodes_to_deleteRs RB t zero_nodet
old_parentt
new_parentRo ( ( R R¢ R¡ s# /Users/lmoncla/src/baltic/baltic.pyt collapseBranches´ sL '=@! . 4
+=@A
c C s | d- k r | j } n | d- k ra t t g | j D] } t | j j ^ q4 g } n | d- k r¾ g } | t k r¾ | t k s t
d | t k r« d GHn | j d q¾ n | d- k rÖ d } n g }
t | d k röx| D]ú} | | j k rÈ| t k rAd | | j
| j t | j | f GHn t | j | t r|
j d | | j | f | t k rÅd |
d GHqÅqït | j | t sÀt | j | t rý|
j d
| | j | f | t k rÅd |
d GHqÅqït | j | t rïg } xj | j | D][ }
t |
t rP| j d |
q't |
t snt |
t r'| j d
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q'q'W|
j d | d j | f | t k rÅd |
d GHqÅqïqõ | t k rõ d | | j
| j f GHqõ qõ Wn | j d k r| t k r d | j
GHn | j d t t | | j } t | d k sjt
d | j
x t | D] \ } } | t k r§d | j
| j
f GHn | j d | d | d | d | d | d | d | | d t | k rw| j d qwqwW| j d n | j d k r¤| t k rW| j d- k sKt
d! | j } n | t k ro| j } n | t k rd" | j
| f GHn | j d# | n t |
d k r| t k rÑd$ | j
GHn d j |
}
d% |
d& }
| j d
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n | t k r d' | j
GHn | j d( | j | | j k r| j d) | t k ri| j d* n | t k r}d+ GHn d, j | Sd- S(. sX Output the topology of the tree with branch lengths and comments to stringself.
cur_node: starting point (default: None, starts at root)
traits: list of keys that will be used to output entries in traits dict of each branch (default: all traits)
numName: boolean, whether encoded (True) or decoded (default: False) tip names will be output
verbose: boolean, debug
nexus: boolean, whether to output newick (default: False) or nexus (True) formatted tree
string_fragment: list of characters that comprise the tree string
s/ Nexus format not a valid option for JSON outputs Exporting to Nexus formats& #NEXUS
Begin trees;
tree TREE1 = [&R] c S s t S( N( R ( RB ( ( s# /Users/lmoncla/src/baltic/baltic.pyRC ý s i s' trait %s available for %s (%s) type: %ss %s="%s"s adding string comment %siÿÿÿÿs %s=%ss adding numeric comment %ss "%s"s %ss %s={%s}t ,s adding range comment %ss trait %s unavailable for %s (%s)R/ s node: %st (s* Node %s does not have traversable childrens moving to child %s of node %sR5 R" R% Rg t nexust string_fragmentRD i t )R s Tip does not have converted names
leaf: %s (%s)s '%s's adding comment to %ss [&t ]s adding branch length to %ss :%8ft ;s
End;t finishedt N( R R6 R2 RX R7 RJ R" t keysR RY Rj R; R R# R t typeRv t strRy t intR RK R0 t enumeratet toStringR$ R% R ( R* R5 R" R% Rg Rª R« RD t jsonRB t commentt trt rangeCommentt valt traverseChildrent cRT t treeName( ( s# /Users/lmoncla/src/baltic/baltic.pyR¶ è s =
+ , "
% 4
c
s± | t k re t | j d k s- t d g | j D]% } t | t r7 | j | j ^ q7 n. g | j D] } t | t ro | j ^ qo f d D } x| j D]ó } | t k rÚ t
| j } n# g | j D] } | j | ^ qä } x© t d t | d D] } x
t | d t | D]j } | | } | | } | | | d k s|| | | | j k r7| j | | | <| j | | | <q7q7WqWq¶ W| S( Ni s3 Tree does not have a translation dict for tip namesc s) i | ] f d D q S( c s+ i | ]! } | k r d n d | q S( g N( R ( t .0R& ( R ( s# /Users/lmoncla/src/baltic/baltic.pys
<dictcomp>K s ( ( R¿ ( t tip_names( R s# /Users/lmoncla/src/baltic/baltic.pys
<dictcomp>K s i ( RY R R8 Rj R7 Rv R R% RI R RJ R t rangeR R (
R* R% RB t tmrcaMatrixt all_childrent lvR R& t tipAt tipB( ( RÀ s# /Users/lmoncla/src/baltic/baltic.pyt allTMRCAsE s" !8. #
+ c C s t | d k s t d t g | D] } | j d k r( | ^ q( d k s t d t g | D] } | j d k rb | ^ qb | t k r¨ d t | GHn d | D } g } | t k rÒ d GHn t j | } x | j D] } | j | k rë | } | t k r!d | j GHn xV | | j k rv| t k r]d | j | | j k f GHn | j | | j
} q$Wqë që W| j | j | t k r¢d
GHn t | } t t
| d d | _ | t k ràd
GHn x? | j D]1 } g | j D] } | | k rý| ^ qý| _ qíWg | j j D] } | | k r/| ^ q/| j _ | j | t k rqd GHn | j | j | S( sz
Reduce the tree to just those tracking a small number of tips.
Returns a new baltic tree object.
i s$ No tips given to reduce the tree to.R s( Embedding contains %d non-leaf branches.s- Preparing branch hash for keeping %d branchesc S s i | ] } | | j q S( ( R# ( R¿ RB ( ( s# /Users/lmoncla/src/baltic/baltic.pys
<dictcomp>d s s Deep copying trees Traversing to root from %ss at %s root: %ss Finished extracting embeddingRO c S s | j S( N( R ( R ( ( s# /Users/lmoncla/src/baltic/baltic.pyRC x s s Pruning untraversed lineagess! Last traversal and branch sorting( R Rj R R RF RG R7 R# R6 R; R! R2 RP RJ RI R0 RL RH RR ( R* t keepRg RB t branch_hasht embeddingt reduced_treet cur_bR½ ( ( s# /Users/lmoncla/src/baltic/baltic.pyt
reduceTree[ sF l
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| j d k S( NR/ ( R ( RB ( ( s# /Users/lmoncla/src/baltic/baltic.pyRC s ( RJ RK R7 ( R* ( ( s# /Users/lmoncla/src/baltic/baltic.pyRI s c C s t S( N( R ( R ( ( s# /Users/lmoncla/src/baltic/baltic.pyRC s c C s[ t t | | j } t | d k r9 t d n t | d k rS | d S| Sd S( Ni s; No branches satisfying function were found amongst branchesi iÿÿÿÿ( RJ RK R7 R t Exception( R* t attrst select( ( s# /Users/lmoncla/src/baltic/baltic.pyt getBranches s c C s¦ d } t t | | j } x~ t | d k r¡ xM t | d d D]6 } | j j j | | j | | j j | qL Wt t | | j } q$ Wd S( s=
Remove internal nodes without any children.
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g | | g d | d | d | | q/ q/ W| S( NRì t unrooteds Unrecognised drawing type "%s"R/ i iÿÿÿÿt colort lwRØ ( Rì Rî ( Rj RK R7 R! R R R0 t plot( R* RÚ R² RÛ Ræ Rç t branchWidthRé RÝ RÞ RB R& R t xpR½ t bRß t ylt yrt yp( ( s# /Users/lmoncla/src/baltic/baltic.pyt plotTree¹ s( 44 8N( R- R. R, R> R@ R R RV RW Rf RY RH Rn R RR Rq R R R R R§ R¶ RÇ RÍ RÐ Rl RI RÔ RL Rà Rë Rø ( ( ( s# /Users/lmoncla/src/baltic/baltic.pyR3 K s6
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data is a tree string, ll (LL) is an instance of a tree object
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Stopped at >>%s<<
string region looks like this: %si R© s %d adding nodei s (\(|,)([0-9]+)(\[|\:)id s %d adding leaf (BEAST) %si s2 (\(|,)('|")*([A-Za-z\_\-\|\.0-9\?\/ ]+)('|"|)(\[)*iÈ s %d adding leaf (non-BEAST) %si t "t 's \)([0-9]+)\[s %d adding multitype node %ss5 (\:)*\[(&[A-Za-z\_\-{}\,0-9\.\%="'\+!# :\/\(\)\&]+)\]s %d comment: %ss! [,&][A-Za-z\_\.0-9]+=[0-9\-Ee\.]+s= [,&][A-Za-z\_\.0-9]+=["|']*[A-Za-z\_0-9\.\+ :\/\(\)\&]+["|']*s4 [,&][A-Za-z\_\.0-9]+={[A-Za-z\_,{}0-9\. :\/\(\)\&]+}s9 [,&][A-Za-z\_\.0-9\%]+={[A-Za-z\.\-0-9eE,"\_ :\/\(\)\&]+}s# \![A-Za-z]+=[A-Za-z0-9# :\/\(\)\&]+t =t +s$ {([0-9]+,[0-9\.\-e]+,[A-Z]+,[A-Z]+)}R¨ R2 iÿÿÿÿs set.probs some other trait: %ss FigTree comment found, ignorings ([A-Za-z\_\-0-9\.]+)(\:|\;)s old school comment found: %st labels (\:)*([0-9\.\-Ee]+)s adding branch length (%d) %.6fR¬ R® N( Rv R³ RY R R3 R R Rj R> t ret matcht groupR@ t stripR t findallR R5 R" Ry R; R´ RJ t mapR R! ( t datat llRg R< t stored_it cerberusR¸ t numericst stringst treelistt setst figtreet valsR¹ R» t
microcerberust codont timingR R t v( ( s# /Users/lmoncla/src/baltic/baltic.pyt make_treeÐ s¾ 1
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make_treeJSON( R t json_translationR Rg R= R RT ( ( R s# /Users/lmoncla/src/baltic/baltic.pyR I s, % s \|([0-9]+\-[0-9]+\-[0-9]+)c C sh d } t | t r' t | d } n | } xe | D]] } | j d } d | k r4 | j d }
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s dimensions ntax=([0-9]+);i s File should contain %d taxaR© s Identified tree strings$ ([0-9]+) ([A-Za-z\-\_\/\.'0-9 \|?]+)i Rù Rú s! Identified tip translation %s: %sR® s tip not captured by regex:s R° t translates- Regular expression failed to find tree stringR R ( RY R Rv R³ R R Rþ R t lowerR´ R R R# R t replaceRj RH RR R Rn R8 Rl R$ R% R; R R[ RW ( R R R t treestring_regexR R Rg t tipFlagt tipst tipNumR R R R R R! R" RB R R# ( ( s# /Users/lmoncla/src/baltic/baltic.pyt loadNexus
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/ t strainR$ t num_dateR c C s¬ d | k r$ d | k sn d | k sn t d d j g d d d d g D] } | | k t k rC | ^ qC | t k r d GHn t | t rÍ t | + } t j | } t | | d | } Wd QXn t t j | | d | } d | k rd | k s'd | k rd | k s't d
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Load a nextstrain JSON by providing either the path to JSON or a file handle.
json_translation is a dictionary that translates JSON attributes to baltic branch attributes (e.g. 'absoluteTime' is called 'num_date' in nextstrain JSONs).
Note that to avoid conflicts in setting node heights you can either define the absolute time of each node or branch lengths (e.g. if you want a substitution tree).
R$ R R s/ JSON translation dictionary missing entries: %ss , R s Reading JSONRg Nsa Cannot use both absolute time and branch length, include only one in json_translation dictionary.g s Traversing and drawing treet fileR t
color_optionst traitNamet color_mapt cmap( Rj R RY R Rv R³ R R· t loadR R7 Rx R" R! R RH Rq Rf RR t dict( R R t json_metaRg t sortt statst entryt json_dataRm R R RB t metadataR3 ( ( s# /Users/lmoncla/src/baltic/baltic.pyt loadJSONÄ s@ n <
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