o RŀgK @sdZddlZddlZddlZddlZddlZddlmZddlm Z ddlm Z ddlm Z ddl m Z ddlmZdd lmZdd lmZd Zgd Zgd ZdZdZdZdgZdZdZdZdZGdddeZ GdddZ!GdddZ"dEddZ#dd Z$dFd"d#Z%d$d%Z&d&d'Z'd(d)Z(d*d+Z)d,d-Z*d.d/Z+d0d1Z,d2d3Z-d4d5Z.Gd6d7d7Z/Gd8d9d9Z0Gd:d;d;Z1zde5d?e d@dAZ7WYdZ5[5n dZ5[5wwdBdAZ7e8dCkrddDl9m:Z:e:dSdS)GzNexus 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 N)reduce)BiopythonDeprecationWarning)BiopythonWarning)File) IUPACData) StandardData)TreeSeqF) charstatelabels charlabels taxlabelstaxsetcharset charpartition taxpartitionmatrixtreeutree translate codonpossettitle)treesdata characterstaxasetscodonsz()[]{}\,;:=*\'"`+-<>?abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ1234567890_z &charsrcodonpositionszH#NEXUS begin data; dimensions ntax=0 nchar=0; format datatype=dna; end; c@seZdZdZdS) NexusErrorz1Provision for the management of Nexus exceptions.N)__name__ __module__ __qualname____doc__r(r(C/var/www/html/myenv/lib/python3.10/site-packages/Bio/Nexus/Nexus.pyr#>sr#c@s`eZdZdZddZddZddZdd Zd d Zd d Z ddZ ddZ ddZ ddZ dS) CharBufferzHelps reading NEXUS-words and characters from a buffer (semi-PRIVATE). This class is not intended for public use (any more). cCs|r t||_dSg|_dSInitialize the class.N)listbuffer)selfstringr(r(r)__init__Hs zCharBuffer.__init__cCs|jr|jdSdS)z+Return the first character from the buffer.rN)r.r/r(r(r)peekOs zCharBuffer.peekcCs d|j}|r|dSdS)zBReturn the first character from the buffer, do not include spaces.rN)joinr.strip)r/br(r(r)peek_nonwhitespaceVszCharBuffer.peek_nonwhitespacecCs|jr |jdSdS)z*Iterate over NEXUS characters in the file.rN)r.popr2r(r(r)__next__^s zCharBuffer.__next__cCs& t|}|dur dS|tvr|Sq)z6Check for next non whitespace character in NEXUS file.TN)next WHITESPACE)r/pr(r(r)next_nonwhitespaceeszCharBuffer.next_nonwhitespacecCs4|jdtvr|jdd|_|jdtvsdSdS)z)Skip whitespace characters in NEXUS file.rN)r.r<r2r(r(r)skip_whitespaceoszCharBuffer.skip_whitespacec Cs\|D])}z|j|}Wn tyYqwd|jd|}|j|d|_|SdS)z@Iterate over the NEXUS file until a target character is reached.r4N)r.index ValueErrorr5)r/targettposfoundr(r(r) next_untilts zCharBuffer.next_untilcCsd|jdt||kS)z#Return a word stored in the buffer.r4N)r5r.len)r/wordr(r(r) peek_wordszCharBuffer.peek_wordcCsg}d}|}|s dS|||dkrd}n |dkrd}n|tvr%|S |}||krD|t|||kr@t|n |rCnn|rN|t|n|rX|tvsX|tvrYn|t|q&d|S)zReturn the next NEXUS word from a string. This deals with single and double quotes, whitespace and punctuation. FN'"Tr4)r>append PUNCTUATIONr3r;r<r5)r/rIquotedfirstcr(r(r) next_words8    zCharBuffer.next_wordcCs d|jS)z.Return the rest of the string without parsing.r4)r5r.r2r(r(r)rest zCharBuffer.restN)r$r%r&r'r1r3r8r:r>r@rGrJrRrSr(r(r(r)r*Bs  &r*c@sJeZdZdZddZddZddZdd Zd d Zd d Z dddZ dS) StepMatrixzCalculate a stepmatrix for weighted parsimony. See : COMBINATORIAL WEIGHTS IN PHYLOGENETIC ANALYSIS - A STATISTICAL PARSIMONY PROCEDURE Wheeler (1990), Cladistics 6:269-275. csXi|_t||_|r|j||jD]fdd|jDD] }||dqqdS)r,csg|]}|kr|qSr(r(.0sxr(r) z'StepMatrix.__init__..rN)rsortedsymbolsrMset)r/r^gapyr(rYr)r1s   zStepMatrix.__init__cCs$||kr ||}}||j||<dS)z+Set a given value in the matrix's position.Nrr/rZravaluer(r(r)r_s zStepMatrix.setcCs,||kr ||}}|j|||7<dS)z6Add the given value to existing, in matrix's position.Nrbrcr(r(r)adds zStepMatrix.addcCstdd|jS)z9Calculate the associations, makes matrix of associations.cSs||SNr()rZrar(r(r)z StepMatrix.sum..)rrvaluesr2r(r(r)sumszStepMatrix.sumcCs2|}|dkr|jD] }|j||<q |S)zlCalculate the transformation matrix. Normalizes the columns of the matrix of associations. r)rjr)r/totalkr(r(r)transformations  zStepMatrix.transformationcCs6|jD]}|j|dkrt|j| |j|<q|S)zCalculate the Phylogenetic weight matrix. Constructed from the logarithmic transformation of the transformation matrix. r)rmathlog)r/rlr(r(r) weightings zStepMatrix.weightingyour_name_herecCsd|t|jf}|dd|jd7}|jD]I}|dd|7}|jD]6}||kr1|d7}q&||kr;||}}n||}}|j||dkrN|d7}q&|d d |j||7}q&|d7}q|d 7}|S) zPrint a stepmatrix.zusertype %s stepmatrix=%d z  z[%s]z . rz inf. z%2.2f ; )rHr^r5ljustr)r/namerrZrax1y1r(r(r)smprints        zStepMatrix.smprintN)rq) r$r%r&r'r1r_rerjrmrprzr(r(r(r)rUs   rUFcCsZ|r|dd}ddd|D}|S|dd}t|tttr+d|d}|S)aReturn a taxon identifier according to NEXUS standard. Wrap quotes around names with punctuation or whitespace, and double single quotes. mrbayes=True: write names without quotes, whitespace or punctuation for the mrbayes software package.  _r4css|] }|tvr|VqdSrf) MRBAYESSAFErWrQr(r(r) zsafename..rKz'')replacer5r_ intersectionr<rN)rwmrbayessafer(r(r)safenames   rcCsh|sdS|dr|ds|dr2|dr2|dd}|dr(|ds|dr2|ds|S)z6Remove quotes and/or double quotes around identifiers.NrKrLr?) startswithendswith)rIr(r(r) quotestrips r-?cCst|}|dkr dS|d}|dkr&|||vr&|d8}|dkr&|||vsd}||kr@|||vr@|d7}||kr@|||vs2||krJ|dkrJdS||fS)zoReturn position of first and last character which is not in skiplist. Skiplist defaults to ['-','?']. rNNr?r)rrrH)sequenceskiplistlengthendstartr(r(r) get_start_endsrcs"tfddDfdddS)zBReturn a sorted list of keys of p sorted by values of p (PRIVATE).c3s|] }|r|VqdSrfr()rWpnr=r(r)r4rz'_sort_keys_by_values..cs|Srfr()rrr(r)rg4rhz&_sort_keys_by_values..)key)r]rr(rr)_sort_keys_by_values2s"rcCs tt|S)zRCheck all values in list are unique and return a pruned and sorted list (PRIVATE).)r]r_)rir(r(r) _make_unique7rTrcCs~||vr=|d}|ddr5d}|ddkr$t|dddd}d|ddd|}|}n|d7}||vs|S)zFReturn a unique name if label is already in previous_labels (PRIVATE)..rcopyr?Nz.copy)splitrintr5)previous_labelslabel label_splitcopy_num new_labelr(r(r) _unique_label<s   rcsfddDS)zHConvert a Seq-object matrix to a plain sequence-string matrix (PRIVATE).csi|] }|t|qSr(strrWrDrr(r) Mz(_seqmatrix2strmatrix..r(rr(rr)_seqmatrix2strmatrixKsrcCsN|sdStt|}g}|dd}||ddt|dkrd}t|D]t\}}||d||kr6q'|dkrUt|dkrU||d|||dkrU||d}q'|d|}t|dkrm|t|ddn(|dkr|d|dd|ddfn|d |dd|dd|f||d}t|dks!d |S) aHCompact lists for Nexus output (PRIVATE). Example ------- >>> _compact4nexus([1, 2, 3, 5, 6, 7, 8, 12, 15, 18, 20]) '2-4 6-9 13-19\\3 21' Transform [1 2 3 5 6 7 8 12 15 18 20] (baseindex 0, used in the Nexus class) into '2-4 6-9 13-19\\3 21' (baseindex 1, used in programs like Paup or MrBayes.). r4Nrg?r?rz%d-%dz%d-%d\%dr{)r]r_rMrH enumeraterr5) orig_list shortlistcliststepirZsubr(r(r)_compact4nexusPs.    0  $$  rc s|sdS|dd}t|ddtdd|Ddk}|r#d_d_d_d_d_j D]\}}|j|d|<j|=q4j D]\}}|j |d|<j |=qLd |t t j ii_|ddD]\fd d jDfd d jD}fd d jD}D]} j| ttj| jjjj7<q|D]} j| tjj 7<q|D]"} tjj ttj| jjjjj| <qʈj|j D]\}}fdd |Djd|<qj r)j si_ j fddj Dt t j j j jd <jrUjsEi_jfddj Dj j 7_ jt|7_qqjd D] } jd | j| <qlS)aCombine 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. Nrr?cSsh|]}|djqS)r?)datatyperWnr(r(r) zcombine..NoneFrcombinedcsg|] }|jvr|qSr()rr)mr(r)r[rzcombine..cg|]}|vr|qSr(r(rbothr(r)r[r\crr(r(rrr(r)r[r\csg|]}|jqSr(ncharrWrZrr(r)r[rcs i|] \}}d||qS)rr()rWtnts)rr(r)r zcombine..csi|] \}}j||qSr(r)rWrrrr(r)r)rdeepcopyrHrr statelabels interleavercharsetsitemstaxsetsr-rangercharpartitionsrrr rrr`missingextendupdatentax) matricesrwmixed_datatypescncsrr combined_onlym_onlyrDrQr()rrrrr)combineysr             $ rc CsV|sdSt|}g}g}d}d}d}t|} |}zt|}Wn ty*d}Ynw|dur0ng||kr;|s;|s;d}nA|sL|sL|sL|dksI|dkrL|}n0|sd|dkrd|tvr_|dkr_|s_d}n|d 7}n|s||d kr||rod}n |d 8}|dkr{td q|dkr|d kr|s|d|g}n||q|r|d ||dkrtd|S)aDelete []-delimited comments out of a file and break into lines separated by ';' (PRIVATE). stripped_text=_kill_comments_and_break_lines(text): Nested and multiline comments are allowed. [ and ] symbols within single or double quotes are ignored, newline ends a quote, all symbols with quotes are treated the same (thus not quoting inside comments like [this character ']' ends a comment]) Special [&...] and [\...] comments remain untouched, if not inside standard comment. Quotes inside special [& and [\ are treated as normal characters, but no nesting inside these special comments allowed (like [& [\ ]]). ';' is deleted from end of line. NOTE: this function is very slow for large files, and obsolete when using C extension cnexus r4FrTNrLrK[r?]z#Nexus formatting error: unmatched ];rrz#Nexus formatting error: unmatched [)iterr; StopIterationSPECIALCOMMENTSr#rMr5) textcontentsnewtextnewline quotelevel speciallevel commlevelt2rDr(r(r)_kill_comments_and_break_linessd       )rcCs^g}|D](}|dddd}|dr||q|dd}|r,||q|S)zAdjust linebreaks to match ';', strip leading/trailing whitespace (PRIVATE). list_of_commandlines=_adjust_lines(input_text) Lines are adjusted so that no linebreaks occur within a commandline (except matrix command line) z rr rr{)rr6lowerrrM)linesformatted_linesliner(r(r) _adjust_liness   rcCs|d}|dkrX|d}|dkrtd|||kr"td|dt||d|}||}||kr?|}|d ||||dd }|d}|dks |S) zGReplace ambigs in xxx(ACG)xxx format by IUPAC ambiguity code (PRIVATE).(r)rz Missing closing parenthesis in: z Missing opening parenthesis in: r4r?N)findr#r5r]upperr)seqrev_ambig_valuesopeningclosingambig ambig_coder(r(r)_replace_parenthesized_ambigs's         rc@seZdZdZddZdS) Commandlinez/Represent a commandline as command and options.cs`i|_gd|_z |dd\|_Wnty0|d|_d|ddYnw|j|_|jtvrE|_dStdkrzS ddfdd t tD}g|D]} |qefd d t tD}|D]}|d |j|d<q||D] }d|j|<qWdStyt d |dwdS) r,Nrrr?rr{= = cs>g|]}|dkr|dkr|tkr|d||dfqS)rrr?rroptionsr(r)r[Ps  z(Commandline.__init__..crr(r(r)indicesr(r)r[Xr\zIncorrect formatting in line: ) rcommandr6rrBr5rSPECIAL_COMMANDSrHrrrr#)r/rrvalued_indicessl token_indicesopttokenr()rrr)r1<s>        zCommandline.__init__Nr$r%r&r'r1r(r(r(r)r9s rc@seZdZdZdddZdS)BlockzARepresent a NEXUS block with block name and list of commandlines.NcCs||_g|_dSr+)r commandlines)r/rr(r(r)r1es zBlock.__init__rfr r(r(r(r)r bsr c@s&eZdZdZdwddZddZddZeeeZd d Z d d Z d dZ ddZ ddZ ddZddZddZddZddZddZdd Zd!d"Zd#d$Zd%d&Zd'd(Zd)d*Zd+d,Zd-d.Zd/d0Zd1d2Zd3d4Zd5d6Zd7d8Z d9d:Z!d;d<Z"d=d>Z#e$d?fd@dAZ%dxdBdCZ&dDdEZ'dwdFdGZ(dHdIZ)dJdKZ*dLdMZ+dNdOZ,    P Q Q  R PdydSdTZ-   Q Q  P P  P U P UdzdVdWZ. Q Q P U Pd{dXdYZ/d|d[d\Z0dwd]d^Z1d}d_d`Z2d~dadbZ3ddddeZ4d}dfdgZ5d}dhdiZ6djdkZ7ddmdnZ8ddodpZ9dqdrZ:ddsdtZ;ddudvZ|r:d}||fVg}n td|rE|||sd Sd S) z>Return a generator for looping through Nexus blocks (PRIVATE).FrbeginTr?zIllegal block nesting in block rzUnmatched 'end'.N)r9rrrr#rM)r/r5inblock blocklinesr6rr(r(r)r0s&    zNexus._get_nexus_blockcCs(t}|j|||_|j|dSrf)r r rMrr)r/rrblockr(r(r)r3s zNexus._unknown_nexus_blockc Csb||||jd}|jD] }z t|d|j|jWqty.td|jddwdS)z$Parse a known Nexus Block (PRIVATE).rr|zUnknown command: r{N)_apply_block_structurerr r(rrr,r#)r/rrr;rr(r(r)r2s    zNexus._parse_nexus_blockcCdSrfr(r/rr(r(r)_titlez Nexus._titlecCr=rfr(r>r(r(r)_linkr@z Nexus._linkcCs4d|vr t|d|_d|vrt|d|_dSdS)Nrr)evalrrr>r(r(r) _dimensionss zNexus._dimensionscCs.d|vrd|_d|vr@d|d|_|jdr!|jds-|jdr5|jdr5|jdd|_|js@t|j|_d |vr|d |_ |j d ksU|j d kr`t j |_ t j|_nO|j d krpt j |_ t j|_n?|j d krddt jd|_ t jd|_n+|j dkri|_ |jstdd|j|_|js|j|j7_ntd|j d|j |j|_|js|j|j|_dd|j D}i|_|D]\}}tdd|D}||jd|<q|j dvrt j|_|j|j vr |j|j|j |j<|j|j |j<n"|j d kr3t j|_|j|j vr,|j|j|j |j<|j|j |j<d|vr?|dd|_d|vrK|dd|_d|vrU|d|_d|vra|dd|_d|vrk|d|_d |vr|d dus|d d!krd|_d"|vrd|_ d#|vrd$|_ dSdS)%NrTr^r4rLrKr?rrr  nucleotidernaproteinDNEQ)BZX*standardzSymbols must be defined when using standard datatype. Please remove any whitespace (spaces, tabs, etc.) between values for symbols as this confuses the Nexus parser.zUnsupported datatype: cSsi|] \}}|dkr||qS)rKr()rWrlvr(r(r)rLsz!Nexus._format..css|]}|VqdSrfr(r~r(r(r)rOsz Nexus._format..)r rDrrr`rrrryesrnotokensF)!rr5rr^rrr-rrrrambiguous_dna_valuesrambiguous_valuesunambiguous_dna_lettersunambiguous_lettersambiguous_rna_valuesunambiguous_rna_lettersprotein_lettersr#valid_charactersrrev_ambiguous_valuesr]ambiguous_dna_lettersrr`ambiguous_rna_lettersrrrrr)r/rrevrlrNrr(r(r)_format s                           z Nexus._formatcC ||_dSrf)r_r>r(r(r)_setu z Nexus._setcCr^rfrr>r(r(r)_optionsxr`zNexus._optionscCr^rf)rr>r(r(r) _eliminate{r`zNexus._eliminatecCsdS)a&Get taxon labels (PRIVATE). As the taxon names are already in the matrix, this is superfluous except for transpose matrices, which are currently unsupported anyway. Thus, we ignore the taxlabels command to make handling of duplicate taxon names easier. Nr(r>r(r(r) _taxlabels~szNexus._taxlabelscCs&dd|jD}|dd}||S)z8Check for presence of taxon in self.taxlabels (PRIVATE).cSsi|] }|dd|qS)r{r|)rrr(r(r)rrz*Nexus._check_taxlabels..r{r|)rrget)r/taxonnextaxanexidr(r(r)_check_taxlabelss  zNexus._check_taxlabelscCsvi|_t|} |}|durdS|j|td}t|}||j|<|}|dur.dS|dkr:td|dq)z$Get labels for characters (PRIVATE).TNset_type,Missing ',' in line r)r r*rR_resolveCHARSETrr>r#)r/roptsw identifierstaterQr(r(r) _charlabelss  zNexus._charlabelscCsi|_i|_t|}|jstd |}|durdS|j|td}t|}||j|<g|j|<| }|dur=dS|dkr|dkrMtd|dt|}|dur_td|d t |j|t |jkrrtd ||j| |t|}|durdS|dkrnq`q) Nz3Symbols must be defined when using character statesTrirk/rlrz Missing character state in line z?Character states exceed number of available symbols in line %s.) r rr*r^r#rRrmrnrr>rHrM)r/rrorprq characterrQrrr(r(r)_charstatelabelssJ     zNexus._charstatelabelscCr=rfr(r>r(r(r) _statelabelsszNexus._statelabelscCsZ|jr|js tdi|_d}d}dd|dD}t|} zt|}WntyD||jkr7tdd||jkrAtd dYn/w|d 7}||jkrY|jsUtd d }d }t |}t | }| }d } |jr|rxd |} n,d t|} n"d |} t| |jkrt|}| d |7} t| |jks|jdkrtt| |j} |d kr| } n$|jr | |j} | dkrnt| d| | | | | d d} qt| D]\} }||jvr||jkr||jkrtd||| fqn1t| } t| D](\} }|dD]}||jvr+||jkr+||jkr+td||| fqq|rN|j|tt|j|}| |j|<|j |n$t|j d|d |}|!|}|rl|j|| 7<ntd|q |jD]}t|j||jkrtd|jt|j||fqvt"|j}t"|j dd}||krt#ddS)z+Create a matrix for NEXUS object (PRIVATE).z+Dimensions must be specified before matrix!rTcSs g|] }|dkr|qSr4)r6rWr|r(r(r)r[rz!Nexus._matrix..rrzNot enough taxa in matrix.NzToo many taxa in matrix.r?z7Too many taxa in matrix - should matrix be interleaved?Fr4rMrzMTaxon %s: Illegal character %s in sequence %s (check dimensions/interleaving)dzZTaxon %s not in first block of interleaved matrix. Check matrix dimensions and interleave.zr# Exception)r/rrorqrrQr(r(r) _translateks&     zNexus._translatecCs||dS)z@Use 'utree' to denote an unrooted tree (ex: clustalx) (PRIVATE).N)_treer>r(r(r)_utreesz Nexus._utreec Cslt|}|dkr|}|}|dkr#td|ddd}d}|dkrn|t|}|dkrEtd ||ddft|}|d } t||d krYd }n|d kr`d}n|dkrht| }|dks-t|||| d} |j r| D],} zt |j t| | jj| | j_Wqttfytd| | jjdw|j| dS)NrLrz"Syntax error in tree description: 2Fg?rr z7Illegal special comment [%s...] in tree description: %srRTUW)rwweightrootedrz/Unable to substitute %s using 'translate' data.)r*r8r>rRr#r;rGfloatrrSr6r get_terminalsrrnoderrerBKeyErrorrrM) r/rrodummyrwrrsymbolspecialrdrrr(r(r)rsX       z Nexus._treecCs:td}||_|D] }|jt||q |j|dS)z2Apply Block structure to the NEXUS file (PRIVATE).r4N)r rr rMrr)r/rrr;rr(r(r)r<s zNexus._apply_block_structurecC$|j|td\}}t||j|<dS)zCreate unique taxset (PRIVATE).riN) _get_indicesTAXSETrr)r/rrwrr(r(r)_taxsetz Nexus._taxsetcCr)z&Create unique character set (PRIVATE).riN)rrnrr)r/rrwsitesr(r(r)_charsetrzNexus._charsetc Ci}d}t|}||}|std|dd} t|}|dus(|dkr@|s@|j|tdd \}} t| ||<d}|dur?n n |d krG| }||7}q||j|<dS) z1Collect taxpartition from a NEXUS file (PRIVATE).Fz"Formatting error in taxpartition: r{r4TNrk:rj separatorrK)r*_name_n_vectorr#r;rrrr) r/rrrrorwrrpsubname subindicesr(r(r) _taxpartition.  zNexus._taxpartitioncs^t|j||fdd|jD}|gks t|dkr(td|d|d|_dS)zRead codon positions from a codons block as written from McClade (PRIVATE). Here codonposset is just a fancy name for a character partition with the name CodonPositions and the partitions N,1,2,3 crr(r(rprev_partitionsr(r)r[r\z&Nexus._codonposset..r?z!Formatting Error in codonposset: r{rN)r-rr{_charpartitionrHr#r)r/r codonnamer(rr) _codonpossets  zNexus._codonpossetcCr=rfr(r>r(r(r)_codesetr@zNexus._codesetc Cr) z6Collect character partition from NEXUS file (PRIVATE).Fz#Formatting error in charpartition: r{r4TNrkrrrK)r*rr#r;rrnrr) r/rrrrorwrrprrr(r(r)rrzNexus._charpartitionrcCsDt|}|j||d}|j||d}|durtd|d||fS)zParse the taxset/charset specification (PRIVATE). e.g. '1 2 3 - 5 dog cat 10 - 20 \\ 3' --> [0,1,2,3,4,'dog','cat',9,12,15,18] )rriNFormatting error in line: r{)r*r _parse_listr#)r/rrjrrorwrr(r(r)r s zNexus._get_indicescCs|}|}|dkr|}|std|dt|}|jdkrL|}|}|}|dkrr)r/rorrSrwopen qualifiercloser(r(r)rs$    zNexus._name_n_vectorc Cs<g}|rz |}|sW|S|j||d}|dkrz|}d}|}|j||d}|tkrO|dkrC|} t|}|t||d|n;t|t sYt|t r_t d||j |}|j |}|j ||d} || nt|t r||n| |qt ytyYdSw|S)zParse a NEXUS list (PRIVATE). e.g. [1, 2, 4-8\\2, dog, cat] --> [1,2,4,6,8,17,21], (assuming dog is taxon no. 17 and cat is taxon no. 21). Trirr?\z:Name if character sets not allowed in range definition: %sN)r8rRrmr>rnrrrr-r-r#rrArMr) r/options_bufferrj plain_listrqrrrhyphen backslashtaxranger(r(r)r-sV(         ' zNexus._parse_listcCsvt|}|s td|tkrfzt|}Wn?tyS|jr9||jvr9|jD]}|j||kr7|YSq(n|jrH||jvrH|j|YStd|dYdSw||jkr]|dStd||jf|t krzt|}Wn)ty| |}|r|YS|j r||j vr|j |YStd|dw|dkr||j kr|j |dStd||j ftd |d ) a+Translate identifier in list into character/taxon index (PRIVATE). Characters (which are referred to by their index in Nexus.py): Plain numbers are returned minus 1 (Nexus indices to python indices) Text identifiers are translated into their indices (if plain character identifiers), the first hit in charlabels is returned (charlabels don't need to be unique) or the range of indices is returned (if names of character sets). Taxa (which are referred to by their unique name in Nexus.py): Plain numbers are translated in their taxon name, underscores and spaces are considered equal. Names are returned unchanged (if plain taxon identifiers), or the names in the corresponding taxon set is returned. z0INTERNAL ERROR: Need type to resolve identifier.zUnknown character identifier: Nr?z-Illegal character identifier: %d>nchar (=%d).zUnknown taxon identifier: rz(Illegal taxon identifier: %d>ntax (=%d).zUnknown set specification: r)rr#rnrrBr rirrrrhrrr)r/rqrjrrl taxlabels_idr(r(r)rmesh         zNexus._resolvecCr=rfr(r>r(r(r) _statesetzNexus._statesetcCr=rfr(r>r(r(r) _changesetrzNexus._changesetcCr=rfr(r>r(r(r)_treesetrzNexus._treesetcCr=rfr(r>r(r(r)_treepartitionrzNexus._treepartitionFr(r4c  s|s|j}|s dS|s|j}rgi} D]Pt|} | fddt|jDt| } |dd} |d} | dkrL|d| dd }n|d}|| <|j||||| || d | d q| S|jd }|j|||||||d | d |S) zWrite a nexus file for each partition in charpartition. Only non-excluded characters and non-deleted taxa are included, just the data block is written. Nc3s |] }|vr|VqdSrfr(r~rr=r(r)rsz4Nexus.write_nexus_data_partitions..z Partition: rrrrr|z.dataF) r)r blocksizerexcludedeletecomment append_setsr) rr)r-rrrrrfindwrite_nexus_data)r/rr)rrrrrrr pfilenames total_excludepcommentdot pfilenamefnr(rr)write_nexus_data_partitionssZ    z!Nexus.write_nexus_data_partitionsTc  ssjs dS|sj}fddDr(tddttj|rS|jvr6td|j|} t| }i}| D]}fdd| |D||<qCfddjD}t j d }t |}t ||d }|r~|r|d d krdSt j |d d }| s|d|r|d|d|d|d||f|djjr|djr|djjr|djjr|djjr|djjr|dj|s|r|d|djrjdt}|ddfdd|Dd|d |s0|r-d!}nj}tfd"d|D}|rd }|D]R}|d|d#|dt ||d kr|D]$}|t|d$|d%|||||t ||d&q[|d&n|d'|t ||7}qBnw|rtd ||D]+}|D] }|t|d$|d%||||||d&q|d&qnA|D]>}||kr|t|d$d&n|t|d$|d%||}td ||D]}|||||d&q~q|d(| rD| r1|jd)d*|jd+d,n|jd-Wd|SWd|SWd|S1sXwY|S).aWrite a nexus file with data and sets block to a file or handle. Character sets and partitions are appended by default, and are adjusted according to excluded characters (i.e. character sets still point to the same sites (not necessarily same positions), without including the deleted characters. - filename - Either a filename as a string (which will be opened, written to and closed), or a handle object (which will be written to but NOT closed). - interleave_by_partition - Optional name of partition (string) - omit_NEXUS - Boolean. If true, the '#NEXUS' line normally at the start of the file is omitted. Returns the filename/handle used to write the data. Ncg|] }|s|qSr(rhrr2r(r)r[rz*Nexus.write_nexus_data..zUnknown taxa: %s, zUnknown partition: crr(r(r~rr(r)r[)r\c g|] }|vr|vr|qSr(r()rWrerrr(r)r[+s)rrrr4rp)modez#NEXUS rz] z begin data; zdimensions ntax=%d nchar=%d; zformat datatype=z respectcasez missing=z gap=z matchchar=z labels=z equate=z interleaverurz charlabels c3s*|]}|ddt|VqdS)r?r{NrrWrl) newcharlabelsr(r)rTs(z)Nexus.write_nexus_data..zmatrix r c3s |] }tt|dVqdS)rN)rHrrrr(r)r^s: rr?rrz [empty] z; end; F)rrrinclude_codonsT)rrr codons_only)rrr)rr)r#r5r_ differencerrrr crop_matrixrHrr'writerrrr`rrrr _adjust_charlabelsr]rmaxrrvrr)r/r)rrrrrinterleave_by_partitionr omit_NEXUSrr codons_block partitionnames newpartitionr=undeletecropped_matrix ntax_adjustednchar_adjustedfhclkeys namelengthseekre taxon_seqr()rrrrrr/r)rs            "    g g ggzNexus.write_nexus_datac sV|js |js |js dS|rdg}ndg}d}gt|jD]}|vr-|d7}dq||q|s|jD]\} } fdd| D} | r[|d t| d t| q<|jD] \} } fd d| D} | r|d t| d d | qa|jD]R\} }|s| t krq|r| t krqt |}i|D]}fdd||D}|r||<qr|r| t krd}nd}|d|t| d fdd|Dfq|j D]8\} }t |}i|D]}fdd||D}|r||<qr|dt| d fdd|Dfq|dt |dkr&dSd |S)zReturn a sets block.r4z begin codonsz begin setsrr?rcg|] }|vr|qSr(r(r~rofflistr(r)r[rz%Nexus.append_sets..zcharset rcs g|] }|vrt|dqS)rrr)rrr(r)r[rztaxset r{crr(r(r~rr(r)r[rrrz %s %s = %src3s.|]}|vr|dt|VqdS)rN)rrWsnrr(r)rsz$Nexus.append_sets..crr(r(rrr(r)r[r\ztaxpartition %s = %sc3s<|]}|vrdt|ddd|DfVqdS)z%s: %sr{css|]}t|VqdSrfrrr(r(r)rz.Nexus.append_sets...N)rr5rrr(r)rszend; rru)rrrrrrMrrrr5CODONPOSITIONSrrrH)r/rrrrrsetsboffsetrQrnscsetrXtsetr=rrnsprr()rrrrrr)rs        zNexus.append_setsr c Cs|s(d|jvr#|jdddvr#d|jdddd}n|jd}t|d<}|jD]/}|dt|dtd t t |j ||D]}|t |j ||||dqKq1Wd|S1slwY|S) zWrite matrix into a fasta file.rrpaupnexusnexdatNz.fasrp>rrr) r)rrr5rrrrrrHrr)r/r)widthrrerr(r(r) export_fastas"    & zNexus.export_fastacCs|s(d|jvr#|jdddvr#d|jdddd}n|jd}t|d*}|d|j|jf|jD]}|t |d|j |d q.Nr?crr(r(rrr(r)r[5r\rcs2g|]\}}|vr|j||fqSr()rRrdr)rWrZr)rr/r(r)r[7s rrr4cSsg|]}|dqS)rr(rVr(r(r)r[f)rrrHrrrrrr`rrrMrRrdr_rr5) r/rrrrconstantre newconstantsiteseqsite intersectcposr(rrrr/r)r -sH "        zNexus.constantcsfddjD}|sdSg|D];}j||}jddkr-|jkr-j}|r>|jkr>|vr=|qfddj |Dqjvrd|rdt dkrdfd dD S) zSummarize character. narrow=True: paup-mode (a c ? --> ac; ? ? ? --> ?) narrow=false: (a c ? --> a c g t -; ? ? ? --> a c g t -) crr(r(rrr(r)r[or\z!Nexus.cstatus..Nrrc3s|] }|vr|VqdSrfr()rWr7)cstatusr(r)r{rz Nexus.cstatus..r?csg|] }|jkr|qSr()rryr2r(r)r[}r) rrrrrdr`rrMrrRrHsort)r/r rnarrowrrDrQr()rrr/r)ris"  z Nexus.cstatusrqc st|j|j}fddt|jDD]+}|||}t|ddD]\}}||ddD] } ||| dq/q#q| j |dS)zCalculate a stepmatrix for weighted parsimony. See Wheeler (1990), Cladistics 6:269-275 and Felsenstein (1981), Biol. J. Linn. Soc. 16:183-196 crr(r(rVrr(r)r[r\z-Nexus.weighted_stepmatrix..Nrr?)rw) rUrTr`rrrrrerrmrprz) r/rwrrrr rrb1b2r(rr)weighted_stepmatrixs zNexus.weighted_stepmatrixcssjfddDrtddtjgkrgfddjD}|s1iSfdd|D}fddtt|D}|gkrRdd |DSd dd d t|DD}tt||Sfd d jDS)z=Return a matrix without deleted taxa and excluded characters.crr(rrr2r(r)r[rz%Nexus.crop_matrix..zUnknown taxa: rcrr(r(rrr(r)r[rcsg|]}t|qSr(rrrr(r)r[r\csg|] \}}|vr|qSr(r()rWrrXrr(r)r[rcSsi|]}|tdqSrxr rr(r(r)rrz%Nexus.crop_matrix..cSg|]}t|qSr(r rVr(r(r)r[r css|]}d|VqdS)r4Nr5rr(r(r)rsz$Nexus.crop_matrix..cs&i|]}|vr|vr||qSr(r(rrr(r)rs ) rr#r5r_rrrzipdict)r/rrrrrsitesmr(rr)rs& zNexus.crop_matrixcs|s|j}t|t|dt}|j||dsiStds)Sfdd|jD}|rCttfdd|Dn ttfdd|Dfddtt D}d dt|D}|rod d|D}t t||S) zReturn a bootstrapped matrix.r)rrcsg|]}|vr|qSr(r(rcmr(r)r[r\z#Nexus.bootstrap..c3s|] }t|VqdSrfrrrr(r)rrz"Nexus.bootstrap..c3s|]}|VqdSrfr(rrr(r)rrcs$g|]}tdtdqS)rr?)randomrandintrHry)rr(r)r[scSg|]}d|qSrxrrr(r(r)r[rcSrr(r rVr(r(r)r[r ) rr-r-r{r rrrrrHr)r/rrr seqobjectsrbootstrapsitesm bootstrapseqsr()rrr) bootstraps*  zNexus.bootstrapcCs|std|jt|}|dkr||j| n |dkr%||j|7}||jvr1t|j|}n|}||jvr._adjustrzIllegal gap position: %dNc3|] }tj|VqdSrfrrrr2r(r)rz#Nexus.insert_gap..rcSr!rxrrr(r(r)r[rz$Nexus.insert_gap..cs g|] \}}|t|fqSr(r )rWrre)mappedr(r)r[r)r*)insertF)rr#r-rrrHrrrrrrrr ) r/rErr*r,rlistedrrXr=spr()r0r/r)r&s&    zNexus.insert_gapcCs|r|rtd|js dSt|j}i}|rF||tjd}|D]}||vrC|||kr:|d7}|||ks0|j||||<q$|S|rt||tjd}|D]}|||krh|d7}|||ks^|j||||<qV|S|jS)z\Return adjusted indices of self.charlabels if characters are excluded or inserted (PRIVATE).z)Can't exclude and insert at the same timeNrr?)r#r r]rrMsysmaxsize)r/rr1rrexcountrQicountr(r(r)r s:        zNexus._adjust_charlabelscsfddt|jDS)z6Return all character indices that are not in charlist.crr(r(r~charlistr(r)r[+r\z Nexus.invert..)rr)r/r:r(r9r)invert)sz Nexus.invertcsHtj|r jtfddjD}fddt|DS)zReturn gap-only sites.c3r-rfr.rr2r(r)r2r/z Nexus.gaponly..cs"g|] \}}t|r|qSr()r_issubset)rWrr )r`r(r)r[3s"z!Nexus.gaponly..)r_r`rerrrr)r/include_missingrr()r`r/r)gaponly-s  z Nexus.gaponlyc Cs|s|j}|j|jg}|s|ddg|jD]O}t|j|}t|}t||d\}}|dkr9|dkr9||}n|d|d|||d}||||d}|t|kr_td|t ||j|<qdS)z{Replace all terminal gaps with missing character. Mixtures like ???------??------- are properly resolved. rN)rrNr?zJIllegal sequence manipulation in Nexus.terminal_gap_to_missing in taxon %s) rr`rrrrrHr RuntimeErrorr ) r/rskip_nrrerrrrr(r(r)terminal_gap_to_missing5s*     zNexus.terminal_gap_to_missingrf)r) NNNFr(r(Nr4F) NNr(r(NFFNFTFT)r(r(FTF)Nr )Nr(r()r(T)rqr(r()r?Frr2)NT)=r$r%r&r'r1r!r"propertyoriginal_taxon_orderrr0r3r2r?rArCr]r_rarbrcrhrsrvrwrrrrr<rrrrrrrnrrrrmrrrrrrrrr r rrrr%r)r&rr;r>rBr(r(r(r)r ks - ' h=~*  8? C - e   <     0 r r?)cnexuszImport of C module failed (z-). Falling back to slow Python implementationcCst|}t|}|Srf)rr)r5rr r(r(r)r.Xsr.cCs>t|}|dks |dkrtd|t|td}|S)Nrrz Unmatched )rEscanfiler#rrchr)r5 decommentedr r(r(r)r._s __main__) run_doctestr2)r);r'rrnrr5r functoolsrBiorrrBio.DatarBio.Nexus.StandardDatarBio.Nexus.TreesrBio.Seqr INTERLEAVErr1rNr}r<rrnrrrrr#r*rUrrrrrrrrrrrrrr r r4rE ImportErrorexr r.r$ Bio._utilsrKr(r(r(r)s        o O )RH) p