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# Copyright 2005-2008 by Frank Kauff & Cymon J. Cox. All rights reserved. 

# This code is part of the Biopython distribution and governed by its 

# license. Please see the LICENSE file that should have been included 

# as part of this package. 

# 

# Bug reports welcome: fkauff@biologie.uni-kl.de or on Biopython's bugzilla. 

"""Nexus 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 

""" 

from __future__ import print_function 

 

from Bio._py3k import zip 

from Bio._py3k import range 

from Bio._py3k import basestring 

 

from functools import reduce 

import copy 

import math 

import random 

import sys 

 

from Bio import File 

from Bio.Alphabet import IUPAC 

from Bio.Data import IUPACData 

from Bio.Seq import Seq 

 

from .Trees import Tree 

 

INTERLEAVE = 70 

SPECIAL_COMMANDS = ['charstatelabels', 'charlabels', 'taxlabels', 'taxset', 

                    'charset', 'charpartition', 'taxpartition', 'matrix', 

                    'tree', 'utree', 'translate', 'codonposset', 'title'] 

KNOWN_NEXUS_BLOCKS = ['trees', 'data', 'characters', 'taxa', 'sets', 'codons'] 

PUNCTUATION = '()[]{}/\,;:=*\'"`+-<>' 

MRBAYESSAFE = 'abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ1234567890_' 

WHITESPACE = ' \t\n' 

#SPECIALCOMMENTS = ['!','&','%','/','\\','@'] #original list of special comments 

SPECIALCOMMENTS = ['&'] # supported special comment ('tree' command), all others are ignored 

CHARSET = 'chars' 

TAXSET = 'taxa' 

CODONPOSITIONS = 'codonpositions' 

DEFAULTNEXUS = '#NEXUS\nbegin data; dimensions ntax=0 nchar=0; format datatype=dna; end; ' 

 

 

class NexusError(Exception): 

    pass 

 

 

class CharBuffer(object): 

    """Helps reading NEXUS-words and characters from a buffer (semi-PRIVATE). 

 

    This class is not intended for public use (any more). 

    """ 

    def __init__(self, string): 

        if string: 

            self.buffer = list(string) 

        else: 

            self.buffer = [] 

 

    def peek(self): 

        if self.buffer: 

            return self.buffer[0] 

        else: 

            return None 

 

    def peek_nonwhitespace(self): 

        b = ''.join(self.buffer).strip() 

        if b: 

            return b[0] 

        else: 

            return None 

 

    def __next__(self): 

        if self.buffer: 

            return self.buffer.pop(0) 

        else: 

            return None 

 

    if sys.version_info[0] < 3: 

        def next(self): 

            """Deprecated Python 2 style alias for Python 3 style __next__ method.""" 

            return self.__next__() 

 

    def next_nonwhitespace(self): 

        while True: 

            p = next(self) 

            if p is None: 

                break 

            if p not in WHITESPACE: 

                return p 

        return None 

 

    def skip_whitespace(self): 

        while self.buffer[0] in WHITESPACE: 

            self.buffer = self.buffer[1:] 

 

    def next_until(self, target): 

        for t in target: 

            try: 

                pos = self.buffer.index(t) 

            except ValueError: 

                pass 

            else: 

                found = ''.join(self.buffer[:pos]) 

                self.buffer = self.buffer[pos:] 

                return found 

        else: 

            return None 

 

    def peek_word(self, word): 

        return ''.join(self.buffer[:len(word)]) == word 

 

    def next_word(self): 

        """Return the next NEXUS word from a string. 

 

        This deals with single and double quotes, whitespace and punctuation. 

        """ 

 

        word = [] 

        quoted = False 

        first = self.next_nonwhitespace()                   # get first character 

        if not first:                                       # return empty if only whitespace left 

            return None 

        word.append(first) 

        if first == "'":                                    # word starts with a quote 

            quoted = "'" 

        elif first == '"': 

            quoted = '"' 

        elif first in PUNCTUATION:                          # if it's punctuation, return immediately 

            return first 

        while True: 

            c = self.peek() 

            if c == quoted:                                 # a quote? 

                word.append(next(self))                     # store quote 

                if self.peek() == quoted:                   # double quote 

                    skip = next(self)                       # skip second quote 

                elif quoted:                                # second single quote ends word 

                    break 

            elif quoted: 

                word.append(next(self))                              # if quoted, then add anything 

            elif not c or c in PUNCTUATION or c in WHITESPACE: 

                # if not quoted and special character, stop 

                break 

            else: 

                word.append(next(self))                    # standard character 

        return ''.join(word) 

 

    def rest(self): 

        """Return the rest of the string without parsing.""" 

        return ''.join(self.buffer) 

 

 

class StepMatrix(object): 

    """Calculate a stepmatrix for weighted parsimony. 

 

    See Wheeler (1990), Cladistics 6:269-275. 

    """ 

 

    def __init__(self, symbols, gap): 

        self.data = {} 

        self.symbols = sorted(symbols) 

        if gap: 

            self.symbols.append(gap) 

        for x in self.symbols: 

            for y in [s for s in self.symbols if s != x]: 

                self.set(x, y, 0) 

 

    def set(self, x, y, value): 

        if x > y: 

            x, y = y, x 

        self.data[x + y] = value 

 

    def add(self, x, y, value): 

        if x > y: 

            x, y = y, x 

        self.data[x + y] += value 

 

    def sum(self): 

        return reduce(lambda x, y:x+y, self.data.values()) 

 

    def transformation(self): 

        total = self.sum() 

        if total != 0: 

            for k in self.data: 

                self.data[k] = self.data[k] / float(total) 

        return self 

 

    def weighting(self): 

        for k in self.data: 

            if self.data[k] != 0: 

                self.data[k] = -math.log(self.data[k]) 

        return self 

 

    def smprint(self, name='your_name_here'): 

        matrix = 'usertype %s stepmatrix=%d\n' % (name, len(self.symbols)) 

        matrix += '        %s\n' % '        '.join(self.symbols) 

        for x in self.symbols: 

            matrix += '[%s]'.ljust(8) % x 

            for y in self.symbols: 

                if x == y: 

                    matrix += ' .       ' 

                else: 

                    if x > y: 

                        x1, y1 = y, x 

                    else: 

                        x1, y1 = x, y 

                    if self.data[x1 + y1] == 0: 

                        matrix += 'inf.     ' 

                    else: 

                        matrix += '%2.2f'.ljust(10) % (self.data[x1 + y1]) 

            matrix += '\n' 

        matrix += ';\n' 

        return matrix 

 

 

def safename(name, mrbayes=False): 

    """Return 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. 

    """ 

    if mrbayes: 

        safe = name.replace(' ', '_') 

        safe = ''.join(c for c in safe if c in MRBAYESSAFE) 

    else: 

        safe = name.replace("'", "''") 

        if set(safe).intersection(set(WHITESPACE+PUNCTUATION)): 

            safe = "'" + safe + "'" 

    return safe 

 

 

def quotestrip(word): 

    """Remove quotes and/or double quotes around identifiers.""" 

    if not word: 

        return None 

    while (word.startswith("'") and word.endswith("'")) or (word.startswith('"') and word.endswith('"')): 

        word = word[1:-1] 

    return word 

 

 

def get_start_end(sequence, skiplist=['-', '?']): 

    """Return position of first and last character which is not in skiplist. 

 

    Skiplist defaults to ['-','?']).""" 

 

    length = len(sequence) 

    if length == 0: 

        return None, None 

    end = length - 1 

    while end >= 0 and (sequence[end] in skiplist): 

        end -= 1 

    start = 0 

    while start < length and (sequence[start] in skiplist): 

        start += 1 

    if start == length and end == -1: # empty sequence 

        return -1, -1 

    else: 

        return start, end 

 

 

def _sort_keys_by_values(p): 

    """Returns a sorted list of keys of p sorted by values of p.""" 

    return sorted((pn for pn in p if p[pn]), key = lambda pn: p[pn]) 

 

 

def _make_unique(l): 

    """Check that all values in list are unique and return a pruned and sorted list.""" 

    return sorted(set(l)) 

 

 

def _unique_label(previous_labels, label): 

    """Returns a unique name if label is already in previous_labels.""" 

    while label in previous_labels: 

        if label.split('.')[-1].startswith('copy'): 

            label = '.'.join(label.split('.')[:-1]) \ 

                  + '.copy' + str(eval('0'+label.split('.')[-1][4:])+1) 

        else: 

            label += '.copy' 

    return label 

 

 

def _seqmatrix2strmatrix(matrix): 

    """Converts a Seq-object matrix to a plain sequence-string matrix.""" 

    return dict((t, str(matrix[t])) for t in matrix) 

 

 

def _compact4nexus(orig_list): 

    """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.). 

    """ 

 

    if not orig_list: 

        return '' 

    orig_list = sorted(set(orig_list)) 

    shortlist = [] 

    clist = orig_list[:] 

    clist.append(clist[-1] + .5) # dummy value makes it easier 

    while len(clist) > 1: 

        step = 1 

        for i, x in enumerate(clist): 

            if x == clist[0] + i*step:   # are we still in the right step? 

                continue 

            elif i == 1 and len(clist) > 3 and clist[i+1] - x == x - clist[0]: 

                # second element, and possibly at least 3 elements to link, 

                # and the next one is in the right step 

                step = x - clist[0] 

            else:   # pattern broke, add all values before current position to new list 

                sub = clist[:i] 

                if len(sub) == 1: 

                    shortlist.append(str(sub[0]+1)) 

                else: 

                    if step == 1: 

                        shortlist.append('%d-%d' % (sub[0]+1, sub[-1]+1)) 

                    else: 

                        shortlist.append('%d-%d\\%d' % (sub[0]+1, sub[-1]+1, step)) 

                clist = clist[i:] 

                break 

    return ' '.join(shortlist) 

 

 

def combine(matrices): 

    """Combine 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. 

    """ 

 

    if not matrices: 

        return None 

    name = matrices[0][0] 

    combined = copy.deepcopy(matrices[0][1]) # initiate with copy of first matrix 

    mixed_datatypes = (len(set(n[1].datatype for n in matrices)) > 1) 

    if mixed_datatypes: 

        # dealing with mixed matrices is application specific. 

        # You take care of that yourself! 

        combined.datatype = 'None' 

    #    raise NexusError('Matrices must be of same datatype') 

    combined.charlabels = None 

    combined.statelabels = None 

    combined.interleave = False 

    combined.translate = None 

 

    # rename taxon sets and character sets and name them with prefix 

    for cn, cs in combined.charsets.items(): 

        combined.charsets['%s.%s' % (name, cn)]=cs 

        del combined.charsets[cn] 

    for tn, ts in combined.taxsets.items(): 

        combined.taxsets['%s.%s' % (name, tn)]=ts 

        del combined.taxsets[tn] 

    # previous partitions usually don't make much sense in combined matrix 

    # just initiate one new partition parted by single matrices 

    combined.charpartitions = {'combined':{name:list(range(combined.nchar))}} 

    for n, m in matrices[1:]:    # add all other matrices 

        both = [t for t in combined.taxlabels if t in m.taxlabels] 

        combined_only = [t for t in combined.taxlabels if t not in both] 

        m_only = [t for t in m.taxlabels if t not in both] 

        for t in both: 

            # concatenate sequences and unify gap and missing character symbols 

            combined.matrix[t] += Seq(str(m.matrix[t]).replace(m.gap, combined.gap).replace(m.missing, combined.missing), combined.alphabet) 

        # replace date of missing taxa with symbol for missing data 

        for t in combined_only: 

            combined.matrix[t] += Seq(combined.missing*m.nchar, combined.alphabet) 

        for t in m_only: 

            combined.matrix[t] = Seq(combined.missing*combined.nchar, combined.alphabet) + \ 

                Seq(str(m.matrix[t]).replace(m.gap, combined.gap).replace(m.missing, combined.missing), combined.alphabet) 

        combined.taxlabels.extend(m_only)    # new taxon list 

        for cn, cs in m.charsets.items(): # adjust character sets for new matrix 

            combined.charsets['%s.%s' % (n, cn)] = [x+combined.nchar for x in cs] 

        if m.taxsets: 

            if not combined.taxsets: 

                combined.taxsets = {} 

            # update taxon sets 

            combined.taxsets.update(dict(('%s.%s' % (n, tn), ts) 

                                         for tn, ts in m.taxsets.items())) 

        # update new charpartition 

        combined.charpartitions['combined'][n] = list(range(combined.nchar, combined.nchar+m.nchar)) 

        # update charlabels 

        if m.charlabels: 

            if not combined.charlabels: 

                combined.charlabels = {} 

            combined.charlabels.update(dict((combined.nchar + i, label) 

                                            for (i, label) in m.charlabels.items())) 

        combined.nchar += m.nchar # update nchar and ntax 

        combined.ntax += len(m_only) 

 

    # some prefer partitions, some charsets: 

    # make separate charset for ecah initial dataset 

    for c in combined.charpartitions['combined']: 

        combined.charsets[c] = combined.charpartitions['combined'][c] 

 

    return combined 

 

 

def _kill_comments_and_break_lines(text): 

    """Delete []-delimited comments out of a file and break into lines separated by ';'. 

 

    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 [&   [\   ]]). 

    ';' ist deleted from end of line. 

 

    NOTE: this function is very slow for large files, and obsolete when using C extension cnexus 

    """ 

    contents = iter(text) 

    newtext = [] 

    newline = [] 

    quotelevel = '' 

    speciallevel = False 

    commlevel = 0 

    #Parse with one character look ahead (for special comments) 

    t2 = next(contents) 

    while True: 

        t = t2 

        try: 

            t2 = next(contents) 

        except StopIteration: 

            t2 = None 

        if t is None: 

            break 

        if t == quotelevel and not (commlevel or speciallevel): 

            # matching quote ends quotation 

            quotelevel = '' 

        elif not quotelevel and not (commlevel or speciallevel) and (t == '"' or t == "'"): 

            # single or double quote starts quotation 

            quotelevel=t 

        elif not quotelevel and t == '[': 

            # opening bracket outside a quote 

            if t2 in SPECIALCOMMENTS and commlevel == 0 and not speciallevel: 

                speciallevel = True 

            else: 

                commlevel += 1 

        elif not quotelevel and t == ']': 

            # closing bracket ioutside a quote 

            if speciallevel: 

                speciallevel = False 

            else: 

                commlevel -= 1 

                if commlevel < 0: 

                    raise NexusError('Nexus formatting error: unmatched ]') 

                continue 

        if commlevel == 0: 

            # copy if we're not in comment 

            if t == ';' and not quotelevel: 

                newtext.append(''.join(newline)) 

                newline=[] 

            else: 

                newline.append(t) 

    #level of comments should be 0 at the end of the file 

    if newline: 

        newtext.append('\n'.join(newline)) 

    if commlevel > 0: 

        raise NexusError('Nexus formatting error: unmatched [') 

    return newtext 

 

 

def _adjust_lines(lines): 

    """Adjust linebreaks to match ';', strip leading/trailing whitespace. 

 

    list_of_commandlines=_adjust_lines(input_text) 

    Lines are adjusted so that no linebreaks occur within a commandline 

    (except matrix command line) 

    """ 

    formatted_lines = [] 

    for l in lines: 

        #Convert line endings 

        l = l.replace('\r\n', '\n').replace('\r', '\n').strip() 

        if l.lower().startswith('matrix'): 

            formatted_lines.append(l) 

        else: 

            l = l.replace('\n', ' ') 

            if l: 

                formatted_lines.append(l) 

    return formatted_lines 

 

 

def _replace_parenthesized_ambigs(seq, rev_ambig_values): 

    """Replaces ambigs in xxx(ACG)xxx format by IUPAC ambiguity code.""" 

 

    opening = seq.find('(') 

    while opening > -1: 

        closing = seq.find(')') 

        if closing < 0: 

            raise NexusError('Missing closing parenthesis in: '+seq) 

        elif closing < opening: 

            raise NexusError('Missing opening parenthesis in: '+seq) 

        ambig = ''.join(sorted(seq[opening+1:closing])) 

        ambig_code = rev_ambig_values[ambig.upper()] 

        if ambig != ambig.upper(): 

            ambig_code = ambig_code.lower() 

        seq = seq[:opening] + ambig_code + seq[closing+1:] 

        opening = seq.find('(') 

    return seq 

 

 

class Commandline(object): 

    """Represent a commandline as command and options.""" 

 

    def __init__(self, line, title): 

        self.options = {} 

        options = [] 

        self.command = None 

        try: 

            #Assume matrix (all other command lines have been stripped of \n) 

            self.command, options = line.strip().split('\n', 1) 

        except ValueError:  # Not matrix 

            #self.command,options=line.split(' ',1)  #no: could be tab or spaces (translate...) 

            self.command = line.split()[0] 

            options=' '.join(line.split()[1:]) 

        self.command = self.command.strip().lower() 

        if self.command in SPECIAL_COMMANDS: 

            # special command that need newlines and order of options preserved 

            self.options = options.strip() 

        else: 

            if len(options) > 0: 

                try: 

                    options = options.replace('=', ' = ').split() 

                    valued_indices = [(n-1, n, n+1) for n in range(len(options)) 

                                      if options[n] == '=' and n != 0 and n != len((options))] 

                    indices = [] 

                    for sl in valued_indices: 

                        indices.extend(sl) 

                    token_indices = [n for n in range(len(options)) if n not in indices] 

                    for opt in valued_indices: 

                        #self.options[options[opt[0]].lower()] = options[opt[2]].lower() 

                        self.options[options[opt[0]].lower()] = options[opt[2]] 

                    for token in token_indices: 

                        self.options[options[token].lower()] = None 

                except ValueError: 

                    raise NexusError('Incorrect formatting in line: %s' % line) 

 

 

class Block(object): 

    """Represent a NEXUS block with block name and list of commandlines.""" 

    def __init__(self, title=None): 

        self.title = title 

        self.commandlines = [] 

 

 

class Nexus(object): 

 

    def __init__(self, input=None): 

        self.ntax = 0                   # number of taxa 

        self.nchar = 0                  # number of characters 

        self.unaltered_taxlabels = []   # taxlabels as the appear in the input file (incl. duplicates, etc.) 

        self.taxlabels = []             # labels for taxa, ordered by their id 

        self.charlabels = None          # ... and for characters 

        self.statelabels = None         # ... and for states 

        self.datatype = 'dna'           # (standard), dna, rna, nucleotide, protein 

        self.respectcase = False        # case sensitivity 

        self.missing = '?'              # symbol for missing characters 

        self.gap = '-'                  # symbol for gap 

        self.symbols = None             # set of symbols 

        self.equate = None              # set of symbol synonyms 

        self.matchchar = None           # matching char for matrix representation 

        self.labels = None              # left, right, no 

        self.transpose = False          # whether matrix is transposed 

        self.interleave = False         # whether matrix is interleaved 

        self.tokens = False             # unsupported 

        self.eliminate = None           # unsupported 

        self.matrix = None              # ... 

        self.unknown_blocks = []        # blocks we don't care about 

        self.taxsets = {} 

        self.charsets = {} 

        self.charpartitions = {} 

        self.taxpartitions = {} 

        self.trees = []                 # list of Trees (instances of Tree class) 

        self.translate = None           # Dict to translate taxon <-> taxon numbers 

        self.structured = []            # structured input representation 

        self.set = {}                   # dict of the set command to set various options 

        self.options = {}               # dict of the options command in the data block 

        self.codonposset = None         # name of the charpartition that defines codon positions 

 

        # some defaults 

        self.options['gapmode'] = 'missing' 

 

        if input: 

            self.read(input) 

        else: 

            self.read(DEFAULTNEXUS) 

 

    def get_original_taxon_order(self): 

        """Included for backwards compatibility (DEPRECATED).""" 

        return self.taxlabels 

 

    def set_original_taxon_order(self, value): 

        """Included for backwards compatibility (DEPRECATED).""" 

        self.taxlabels = value 

 

    original_taxon_order = property(get_original_taxon_order, set_original_taxon_order) 

 

    def read(self, input): 

        """Read and parse NEXUS input (a filename, file-handle, or string).""" 

 

        # 1. Assume we have the name of a file in the execution dir or a 

        # file-like object. 

        # Note we need to add parsing of the path to dir/filename 

        try: 

            with File.as_handle(input, 'rU') as fp: 

                file_contents = fp.read() 

                self.filename = getattr(fp, 'name', 'Unknown_nexus_file') 

        except (TypeError, IOError, AttributeError): 

            #2 Assume we have a string from a fh.read() 

            if isinstance(input, basestring): 

                file_contents = input 

                self.filename = 'input_string' 

            else: 

                print(input.strip()[:50]) 

                raise NexusError('Unrecognized input: %s ...' % input[:100]) 

        file_contents = file_contents.strip() 

        if file_contents.startswith('#NEXUS'): 

            file_contents = file_contents[6:] 

        commandlines = _get_command_lines(file_contents) 

        # get rid of stupid 'NEXUS token - in merged treefiles, this might appear multiple times' 

        for i, cl in enumerate(commandlines): 

            try: 

                if cl[:6].upper() == '#NEXUS': 

                    commandlines[i] = cl[6:].strip() 

            except: 

                pass 

        # now loop through blocks (we parse only data in known blocks, thus ignoring non-block commands 

        nexus_block_gen = self._get_nexus_block(commandlines) 

        while True: 

            try: 

                title, contents = next(nexus_block_gen) 

            except StopIteration: 

                break 

            if title in KNOWN_NEXUS_BLOCKS: 

                self._parse_nexus_block(title, contents) 

            else: 

                self._unknown_nexus_block(title, contents) 

 

    def _get_nexus_block(self, file_contents): 

        """Generator for looping through Nexus blocks.""" 

        inblock = False 

        blocklines = [] 

        while file_contents: 

            cl = file_contents.pop(0) 

            if cl.lower().startswith('begin'): 

                if not inblock: 

                    inblock = True 

                    title = cl.split()[1].lower() 

                else: 

                    raise NexusError('Illegal block nesting in block %s' % title) 

            elif cl.lower().startswith('end'): 

                if inblock: 

                    inblock = False 

                    yield title, blocklines 

                    blocklines = [] 

                else: 

                    raise NexusError('Unmatched \'end\'.') 

            elif inblock: 

                blocklines.append(cl) 

 

    def _unknown_nexus_block(self, title, contents): 

        block = Block() 

        block.commandlines.append(contents) 

        block.title = title 

        self.unknown_blocks.append(block) 

 

    def _parse_nexus_block(self, title, contents): 

        """Parse a known Nexus Block (PRIVATE).""" 

        # attached the structered block representation 

        self._apply_block_structure(title, contents) 

        #now check for taxa,characters,data blocks. If this stuff is defined more than once 

        #the later occurences will override the previous ones. 

        block = self.structured[-1] 

        for line in block.commandlines: 

            try: 

                getattr(self, '_' + line.command)(line.options) 

            except AttributeError: 

                raise NexusError('Unknown command: %s ' % line.command) 

 

    def _title(self, options): 

        pass 

 

    def _link(self, options): 

        pass 

 

    def _dimensions(self, options): 

        if 'ntax' in options: 

            self.ntax = eval(options['ntax']) 

        if 'nchar' in options: 

            self.nchar = eval(options['nchar']) 

 

    def _format(self, options): 

        # print options 

        # we first need to test respectcase, then symbols (which depends on respectcase) 

        # then datatype (which, if standard, depends on symbols and respectcase in order to generate 

        # dicts for ambiguous values and alphabet 

        if 'respectcase' in options: 

            self.respectcase = True 

        # adjust symbols to for respectcase 

        if 'symbols' in options: 

            self.symbols = options['symbols'] 

            if (self.symbols.startswith('"') and self.symbols.endswith('"')) or\ 

            (self.symbold.startswith("'") and self.symbols.endswith("'")): 

                self.symbols = self.symbols[1:-1].replace(' ', '') 

            if not self.respectcase: 

                self.symbols = self.symbols.lower() + self.symbols.upper() 

                self.symbols = list(set(self.symbols)) 

        if 'datatype' in options: 

            self.datatype = options['datatype'].lower() 

            if self.datatype == 'dna' or self.datatype == 'nucleotide': 

                self.alphabet = IUPAC.IUPACAmbiguousDNA() # fresh instance! 

                self.ambiguous_values = IUPACData.ambiguous_dna_values.copy() 

                self.unambiguous_letters = IUPACData.unambiguous_dna_letters 

            elif self.datatype == 'rna': 

                self.alphabet = IUPAC.IUPACAmbiguousDNA() # fresh instance! 

                self.ambiguous_values = IUPACData.ambiguous_rna_values.copy() 

                self.unambiguous_letters = IUPACData.unambiguous_rna_letters 

            elif self.datatype == 'protein': 

                #TODO - Should this not be ExtendedIUPACProtein? 

                self.alphabet = IUPAC.IUPACProtein() # fresh instance 

                self.ambiguous_values = {'B':'DN', 'Z':'EQ', 'X':IUPACData.protein_letters} 

                # that's how PAUP handles it 

                self.unambiguous_letters = IUPACData.protein_letters + '*'  # stop-codon 

            elif self.datatype == 'standard': 

                raise NexusError('Datatype standard is not yet supported.') 

                #self.alphabet = None 

                #self.ambiguous_values = {} 

                #if not self.symbols: 

                #    self.symbols = '01' # if nothing else defined, then 0 and 1 are the default states 

                #self.unambiguous_letters = self.symbols 

            else: 

                raise NexusError('Unsupported datatype: ' + self.datatype) 

            self.valid_characters = ''.join(self.ambiguous_values) + self.unambiguous_letters 

            if not self.respectcase: 

                self.valid_characters = self.valid_characters.lower() + self.valid_characters.upper() 

            #we have to sort the reverse ambig coding dict key characters: 

            #to be sure that it's 'ACGT':'N' and not 'GTCA':'N' 

            rev=dict((i[1], i[0]) for i in self.ambiguous_values.items() if i[0]!='X') 

            self.rev_ambiguous_values = {} 

            for (k, v) in rev.items(): 

                key = sorted(c for c in k) 

                self.rev_ambiguous_values[''.join(key)] = v 

        #overwrite symbols for datype rna,dna,nucleotide 

        if self.datatype in ['dna', 'rna', 'nucleotide']: 

            self.symbols = self.alphabet.letters 

            if self.missing not in self.ambiguous_values: 

                self.ambiguous_values[self.missing] = self.unambiguous_letters+self.gap 

            self.ambiguous_values[self.gap] = self.gap 

        elif self.datatype == 'standard': 

            if not self.symbols: 

                self.symbols = ['1', '0'] 

        if 'missing' in options: 

            self.missing = options['missing'][0] 

        if 'gap' in options: 

            self.gap = options['gap'][0] 

        if 'equate' in options: 

            self.equate = options['equate'] 

        if 'matchchar' in options: 

            self.matchchar = options['matchchar'][0] 

        if 'labels' in options: 

            self.labels = options['labels'] 

        if 'transpose' in options: 

            raise NexusError('TRANSPOSE is not supported!') 

            self.transpose = True 

        if 'interleave' in options: 

            if options['interleave'] is None or options['interleave'].lower() == 'yes': 

                self.interleave = True 

        if 'tokens' in options: 

            self.tokens = True 

        if 'notokens' in options: 

            self.tokens = False 

 

    def _set(self, options): 

        self.set = options 

 

    def _options(self, options): 

        self.options = options 

 

    def _eliminate(self, options): 

        self.eliminate = options 

 

    def _taxlabels(self, options): 

        """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. 

        """ 

        pass 

        #self.taxlabels = [] 

        #opts = CharBuffer(options) 

        #while True: 

        #    taxon = quotestrip(opts.next_word()) 

        #    if not taxon: 

        #        break 

        #    self.taxlabels.append(taxon) 

 

    def _check_taxlabels(self, taxon): 

        """Check for presence of taxon in self.taxlabels.""" 

        # According to NEXUS standard, underscores shall be treated as spaces..., 

        # so checking for identity is more difficult 

        nextaxa = dict((t.replace(' ', '_'), t) for t in self.taxlabels) 

        nexid = taxon.replace(' ', '_') 

        return nextaxa.get(nexid) 

 

    def _charlabels(self, options): 

        self.charlabels = {} 

        opts = CharBuffer(options) 

        while True: 

            # get id and state 

            w = opts.next_word() 

            if w is None: # McClade saves and reads charlabel-lists with terminal comma?! 

                break 

            identifier = self._resolve(w, set_type=CHARSET) 

            state = quotestrip(opts.next_word()) 

            self.charlabels[identifier] = state 

            # check for comma or end of command 

            c = opts.next_nonwhitespace() 

            if c is None: 

                break 

            elif c != ',': 

                raise NexusError('Missing \',\' in line %s.' % options) 

 

    def _charstatelabels(self, options): 

        # warning: charstatelabels supports only charlabels-syntax! 

        self._charlabels(options) 

 

    def _statelabels(self, options): 

        #self.charlabels = options 

        #print 'Command statelabels is not supported and will be ignored.' 

        pass 

 

    def _matrix(self, options): 

        if not self.ntax or not self.nchar: 

            raise NexusError('Dimensions must be specified before matrix!') 

        self.matrix = {} 

        taxcount = 0 

        first_matrix_block = True 

 

        #eliminate empty lines and leading/trailing whitespace 

        lines = [l.strip() for l in options.split('\n') if l.strip() != ''] 

        lineiter = iter(lines) 

        while True: 

            try: 

                l = next(lineiter) 

            except StopIteration: 

                if taxcount < self.ntax: 

                    raise NexusError('Not enough taxa in matrix.') 

                elif taxcount > self.ntax: 

                    raise NexusError('Too many taxa in matrix.') 

                else: 

                    break 

            # count the taxa and check for interleaved matrix 

            taxcount += 1 

            ##print taxcount 

            if taxcount > self.ntax: 

                if not self.interleave: 

                    raise NexusError('Too many taxa in matrix - should matrix be interleaved?') 

                else: 

                    taxcount = 1 

                    first_matrix_block = False 

            #get taxon name and sequence 

            linechars = CharBuffer(l) 

            id = quotestrip(linechars.next_word()) 

            l = linechars.rest().strip() 

            chars = '' 

            if self.interleave: 

                #interleaved matrix 

                #print 'In interleave' 

                if l: 

                    chars = ''.join(l.split()) 

                else: 

                    chars = ''.join(next(lineiter).split()) 

            else: 

                #non-interleaved matrix 

                chars = ''.join(l.split()) 

                while len(chars)<self.nchar: 

                    l = next(lineiter) 

                    chars += ''.join(l.split()) 

            iupac_seq = Seq(_replace_parenthesized_ambigs(chars, self.rev_ambiguous_values), self.alphabet) 

            #first taxon has the reference sequence if matchhar is used 

            if taxcount == 1: 

                refseq = iupac_seq 

            else: 

                if self.matchchar: 

                    while True: 

                        p = str(iupac_seq).find(self.matchchar) 

                        if p == -1: 

                            break 

                        iupac_seq = Seq(str(iupac_seq)[:p]+refseq[p]+str(iupac_seq)[p+1:], self.alphabet) 

            #check for invalid characters 

            for i, c in enumerate(str(iupac_seq)): 

                if c not in self.valid_characters and c != self.gap and c != self.missing: 

                    raise NexusError("Taxon %s: Illegal character %s in sequence %s " 

                                     "(check dimensions/interleaving)" % (id, c, iupac_seq)) 

            #add sequence to matrix 

            if first_matrix_block: 

                self.unaltered_taxlabels.append(id) 

                id = _unique_label(list(self.matrix.keys()), id) 

                self.matrix[id] = iupac_seq 

                self.taxlabels.append(id) 

            else: 

                # taxon names need to be in the same order in each interleaved block 

                id = _unique_label(self.taxlabels[:taxcount-1], id) 

                taxon_present = self._check_taxlabels(id) 

                if taxon_present: 

                    self.matrix[taxon_present] += iupac_seq 

                else: 

                    raise NexusError("Taxon %s not in first block of interleaved " 

                                     "matrix. Check matrix dimensions and interleave." % id) 

        #check all sequences for length according to nchar 

        for taxon in self.matrix: 

            if len(self.matrix[taxon]) != self.nchar: 

                raise NexusError('Matrix Nchar %d does not match data length (%d) for taxon %s' 

                                 % (self.nchar, len(self.matrix[taxon]), taxon)) 

        #check that taxlabels is identical with matrix.keys. If not, it's a problem 

        matrixkeys = sorted(self.matrix) 

        taxlabelssort = sorted(self.taxlabels[:]) 

        assert matrixkeys == taxlabelssort, \ 

            "ERROR: TAXLABELS must be identical with MATRIX. " + \ 

            "Please Report this as a bug, and send in data file." 

 

    def _translate(self, options): 

        self.translate = {} 

        opts = CharBuffer(options) 

        while True: 

            try: 

                # get id and state 

                identifier = int(opts.next_word()) 

                label = quotestrip(opts.next_word()) 

                self.translate[identifier] = label 

                # check for comma or end of command 

                c = opts.next_nonwhitespace() 

                if c is None: 

                    break 

                elif c != ',': 

                    raise NexusError('Missing \',\' in line %s.' % options) 

            except NexusError: 

                raise 

            except: 

                raise NexusError('Format error in line %s.' % options) 

 

    def _utree(self, options): 

        """Some software (clustalx) uses 'utree' to denote an unrooted tree.""" 

        self._tree(options) 

 

    def _tree(self, options): 

        opts = CharBuffer(options) 

        if opts.peek_nonwhitespace() == '*': 

            # a star can be used to make it the default tree in some software packages 

            dummy = opts.next_nonwhitespace() 

        name = opts.next_word() 

        if opts.next_nonwhitespace() != '=': 

            raise NexusError('Syntax error in tree description: %s' 

                             % options[:50]) 

        rooted = False 

        weight = 1.0 

        while opts.peek_nonwhitespace() == '[': 

            open = opts.next_nonwhitespace() 

            symbol = next(opts) 

            if symbol != '&': 

                raise NexusError('Illegal special comment [%s...] in tree description: %s' 

                                 % (symbol, options[:50])) 

            special = next(opts) 

            value = opts.next_until(']') 

            closing = next(opts) 

            if special == 'R': 

                rooted = True 

            elif special == 'U': 

                rooted = False 

            elif special == 'W': 

                weight = float(value) 

        tree = Tree(name=name, weight=weight, rooted=rooted, tree=opts.rest().strip()) 

        # if there's an active translation table, translate 

        if self.translate: 

            for n in tree.get_terminals(): 

                try: 

                    tree.node(n).data.taxon=safename(self.translate[int(tree.node(n).data.taxon)]) 

                except (ValueError, KeyError): 

                    raise NexusError('Unable to substitute %s using \'translate\' data.' 

                                     % tree.node(n).data.taxon) 

        self.trees.append(tree) 

 

    def _apply_block_structure(self, title, lines): 

        block = Block('') 

        block.title = title 

        for line in lines: 

            block.commandlines.append(Commandline(line, title)) 

        self.structured.append(block) 

 

    def _taxset(self, options): 

        name, taxa = self._get_indices(options, set_type=TAXSET) 

        self.taxsets[name] = _make_unique(taxa) 

 

    def _charset(self, options): 

        name, sites = self._get_indices(options, set_type=CHARSET) 

        self.charsets[name] = _make_unique(sites) 

 

    def _taxpartition(self, options): 

        taxpartition = {} 

        quotelevel = False 

        opts = CharBuffer(options) 

        name=self._name_n_vector(opts) 

        if not name: 

            raise NexusError('Formatting error in taxpartition: %s ' % options) 

        # now collect thesubbpartitions and parse them 

        # subpartitons separated by commas - which unfortunately could be part of a quoted identifier... 

        # this is rather unelegant, but we have to avoid double-parsing and potential change of special nexus-words 

        sub = '' 

        while True: 

            w = next(opts) 

            if w is None or (w == ',' and not quotelevel): 

                subname, subindices = self._get_indices(sub, set_type=TAXSET, separator=':') 

                taxpartition[subname] = _make_unique(subindices) 

                sub = '' 

                if w is None: 

                    break 

            else: 

                if w == "'": 

                    quotelevel = not quotelevel 

                sub += w 

        self.taxpartitions[name] = taxpartition 

 

    def _codonposset(self, options): 

        """Read codon positions from a codons block as written from McClade. 

 

        Here codonposset is just a fancy name for a character partition with 

        the name CodonPositions and the partitions N,1,2,3 

        """ 

 

        prev_partitions = list(self.charpartitions.keys()) 

        self._charpartition(options) 

        # mcclade calls it CodonPositions, but you never know... 

        codonname = [n for n in self.charpartitions if n not in prev_partitions] 

        if codonname == [] or len(codonname) > 1: 

            raise NexusError('Formatting Error in codonposset: %s ' % options) 

        else: 

            self.codonposset = codonname[0] 

 

    def _codeset(self, options): 

        pass 

 

    def _charpartition(self, options): 

        charpartition = {} 

        quotelevel = False 

        opts = CharBuffer(options) 

        name = self._name_n_vector(opts) 

        if not name: 

            raise NexusError('Formatting error in charpartition: %s ' % options) 

        # now collect thesubbpartitions and parse them 

        # subpartitons separated by commas - which unfortunately could be part of a quoted identifier... 

        sub = '' 

        while True: 

            w = next(opts) 

            if w is None or (w == ',' and not quotelevel): 

                subname, subindices = self._get_indices(sub, set_type=CHARSET, separator=':') 

                charpartition[subname] = _make_unique(subindices) 

                sub = '' 

                if w is None: 

                    break 

            else: 

                if w == "'": 

                    quotelevel = not quotelevel 

                sub += w 

        self.charpartitions[name]=charpartition 

 

    def _get_indices(self, options, set_type=CHARSET, separator='='): 

        """Parse 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] 

        """ 

        opts = CharBuffer(options) 

        name = self._name_n_vector(opts, separator=separator) 

        indices = self._parse_list(opts, set_type=set_type) 

        if indices is None: 

            raise NexusError('Formatting error in line: %s ' % options) 

        return name, indices 

 

    def _name_n_vector(self, opts, separator='='): 

        """Extract name and check that it's not in vector format.""" 

        rest = opts.rest() 

        name = opts.next_word() 

        # we ignore * before names 

        if name == '*': 

            name = opts.next_word() 

        if not name: 

            raise NexusError('Formatting error in line: %s ' % rest) 

        name = quotestrip(name) 

        if opts.peek_nonwhitespace == '(': 

            open = opts.next_nonwhitespace() 

            qualifier = open.next_word() 

            close = opts.next_nonwhitespace() 

            if qualifier.lower() == 'vector': 

                raise NexusError('Unsupported VECTOR format in line %s' 

                                 % (opts)) 

            elif qualifier.lower() != 'standard': 

                raise NexusError('Unknown qualifier %s in line %s' 

                                 % (qualifier, opts)) 

        if opts.next_nonwhitespace() != separator: 

            raise NexusError('Formatting error in line: %s ' % rest) 

        return name 

 

    def _parse_list(self, options_buffer, set_type): 

        """Parse 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). 

        """ 

        plain_list = [] 

        if options_buffer.peek_nonwhitespace(): 

            try: 

                # capture all possible exceptions and treat them as formatting 

                # errors, if they are not NexusError 

                while True: 

                    identifier = options_buffer.next_word() # next list element 

                    if not identifier: # end of list? 

                        break 

                    start = self._resolve(identifier, set_type=set_type) 

                    if options_buffer.peek_nonwhitespace() == '-': # followd by - 

                        end = start 

                        step = 1 

                        # get hyphen and end of range 

                        hyphen = options_buffer.next_nonwhitespace() 

                        end = self._resolve(options_buffer.next_word(), set_type=set_type) 

                        if set_type == CHARSET: 

                            if options_buffer.peek_nonwhitespace() == '\\': # followd by \ 

                                                                                         \ 

                                backslash = options_buffer.next_nonwhitespace() 

                                step = int(options_buffer.next_word()) # get backslash and step 

                            plain_list.extend(range(start, end+1, step)) 

                        else: 

                            if isinstance(start, list) or isinstance(end, list): 

                                raise NexusError('Name if character sets not allowed in range definition: %s' 

                                                 % identifier) 

                            start = self.taxlabels.index(start) 

                            end = self.taxlabels.index(end) 

                            taxrange = self.taxlabels[start:end+1] 

                            plain_list.extend(taxrange) 

                    else: 

                        if isinstance(start, list):           # start was the name of charset or taxset 

                            plain_list.extend(start) 

                        else:                           # start was an ordinary identifier 

                            plain_list.append(start) 

            except NexusError: 

                raise 

            except: 

                return None 

        return plain_list 

 

    def _resolve(self, identifier, set_type=None): 

        """Translate identifier in list into character/taxon index. 

 

        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. 

        """ 

        identifier = quotestrip(identifier) 

        if not set_type: 

            raise NexusError('INTERNAL ERROR: Need type to resolve identifier.') 

        if set_type == CHARSET: 

            try: 

                n = int(identifier) 

            except ValueError: 

                if self.charlabels and identifier in self.charlabels.values(): 

                    for k in self.charlabels: 

                        if self.charlabels[k] == identifier: 

                            return k 

                elif self.charsets and identifier in self.charsets: 

                    return self.charsets[identifier] 

                else: 

                    raise NexusError('Unknown character identifier: %s' 

                                     % identifier) 

            else: 

                if n <= self.nchar: 

                    return n-1 

                else: 

                    raise NexusError('Illegal character identifier: %d>nchar (=%d).' 

                                     % (identifier, self.nchar)) 

        elif set_type == TAXSET: 

            try: 

                n = int(identifier) 

            except ValueError: 

                taxlabels_id = self._check_taxlabels(identifier) 

                if taxlabels_id: 

                    return taxlabels_id 

                elif self.taxsets and identifier in self.taxsets: 

                    return self.taxsets[identifier] 

                else: 

                    raise NexusError('Unknown taxon identifier: %s' 

                                     % identifier) 

            else: 

                if n > 0 and n <= self.ntax: 

                    return self.taxlabels[n-1] 

                else: 

                    raise NexusError('Illegal taxon identifier: %d>ntax (=%d).' 

                                     % (identifier, self.ntax)) 

        else: 

            raise NexusError('Unknown set specification: %s.'% set_type) 

 

    def _stateset(self, options): 

        #Not implemented 

        pass 

 

    def _changeset(self, options): 

        #Not implemented 

        pass 

 

    def _treeset(self, options): 

        #Not implemented 

        pass 

 

    def _treepartition(self, options): 

        #Not implemented 

        pass 

 

    def write_nexus_data_partitions(self, matrix=None, filename=None, blocksize=None, 

                                    interleave=False, exclude=[], delete=[], 

                                    charpartition=None, comment='', mrbayes=False): 

        """Writes a nexus file for each partition in charpartition. 

 

        Only non-excluded characters and non-deleted taxa are included, 

        just the data block is written. 

        """ 

 

        if not matrix: 

            matrix = self.matrix 

        if not matrix: 

            return 

        if not filename: 

            filename = self.filename 

        if charpartition: 

            pfilenames = {} 

            for p in charpartition: 

                total_exclude = [] + exclude 

                total_exclude.extend(c for c in range(self.nchar) if c not in charpartition[p]) 

                total_exclude = _make_unique(total_exclude) 

                pcomment = comment + '\nPartition: ' + p + '\n' 

                dot = filename.rfind('.') 

                if dot > 0: 

                    pfilename = filename[:dot] + '_' + p + '.data' 

                else: 

                    pfilename = filename+'_'+p 

                pfilenames[p] = pfilename 

                self.write_nexus_data(filename=pfilename, matrix=matrix, blocksize=blocksize, 

                                      interleave=interleave, exclude=total_exclude, delete=delete, 

                                      comment=pcomment, append_sets=False, mrbayes=mrbayes) 

            return pfilenames 

        else: 

            fn=self.filename+'.data' 

            self.write_nexus_data(filename=fn, matrix=matrix, blocksize=blocksize, 

                                  interleave=interleave, exclude=exclude, delete=delete, 

                                  comment=comment, append_sets=False, mrbayes=mrbayes) 

            return fn 

 

    def write_nexus_data(self, filename=None, matrix=None, exclude=[], delete=[], 

                         blocksize=None, interleave=False, interleave_by_partition=False, 

                         comment=None, omit_NEXUS=False, append_sets=True, mrbayes=False, 

                         codons_block=True): 

        """Writes 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. 

        """ 

        if not matrix: 

            matrix = self.matrix 

        if not matrix: 

            return 

        if not filename: 

            filename = self.filename 

        if [t for t in delete if not self._check_taxlabels(t)]: 

            raise NexusError('Unknown taxa: %s' 

                             % ', '.join(set(delete).difference(set(self.taxlabels)))) 

        if interleave_by_partition: 

            if not interleave_by_partition in self.charpartitions: 

                raise NexusError('Unknown partition: %r' % interleave_by_partition) 

            else: 

                partition = self.charpartitions[interleave_by_partition] 

                # we need to sort the partition names by starting position before we exclude characters 

                names = _sort_keys_by_values(partition) 

                newpartition = {} 

                for p in partition: 

                    newpartition[p] = [c for c in partition[p] if c not in exclude] 

        # how many taxa and how many characters are left? 

        undelete = [taxon for taxon in self.taxlabels if taxon in matrix and taxon not in delete] 

        cropped_matrix = _seqmatrix2strmatrix(self.crop_matrix(matrix, exclude=exclude, delete=delete)) 

        ntax_adjusted = len(undelete) 

        nchar_adjusted = len(cropped_matrix[undelete[0]]) 

        if not undelete or (undelete and undelete[0] == ''): 

            return 

 

        with File.as_handle(filename, mode='w') as fh: 

            if not omit_NEXUS: 

                fh.write('#NEXUS\n') 

            if comment: 

                fh.write('[' + comment + ']\n') 

            fh.write('begin data;\n') 

            fh.write('\tdimensions ntax=%d nchar=%d;\n' % (ntax_adjusted, nchar_adjusted)) 

            fh.write('\tformat datatype=' + self.datatype) 

            if self.respectcase: 

                fh.write(' respectcase') 

            if self.missing: 

                fh.write(' missing=' + self.missing) 

            if self.gap: 

                fh.write(' gap=' + self.gap) 

            if self.matchchar: 

                fh.write(' matchchar=' + self.matchchar) 

            if self.labels: 

                fh.write(' labels=' + self.labels) 

            if self.equate: 

                fh.write(' equate=' + self.equate) 

            if interleave or interleave_by_partition: 

                fh.write(' interleave') 

            fh.write(';\n') 

            #if self.taxlabels: 

            #    fh.write('taxlabels '+' '.join(self.taxlabels)+';\n') 

            if self.charlabels: 

                newcharlabels = self._adjust_charlabels(exclude=exclude) 

                clkeys = sorted(newcharlabels) 

                fh.write('charlabels ' 

                         + ', '.join("%s %s" % (k+1, safename(newcharlabels[k])) for k in clkeys) 

                         + ';\n') 

            fh.write('matrix\n') 

            if not blocksize: 

                if interleave: 

                    blocksize = 70 

                else: 

                    blocksize = self.nchar 

            # delete deleted taxa and ecxclude excluded characters... 

            namelength = max(len(safename(t, mrbayes=mrbayes)) for t in undelete) 

            if interleave_by_partition: 

                # interleave by partitions, but adjust partitions with regard to excluded characters 

                seek = 0 

                for p in names: 

                    fh.write('[%s: %s]\n' % (interleave_by_partition, p)) 

                    if len(newpartition[p]) > 0: 

                        for taxon in undelete: 

                            fh.write(safename(taxon, mrbayes=mrbayes).ljust(namelength+1)) 

                            fh.write(cropped_matrix[taxon][seek:seek+len(newpartition[p])]+'\n') 

                        fh.write('\n') 

                    else: 

                        fh.write('[empty]\n\n') 

                    seek += len(newpartition[p]) 

            elif interleave: 

                for seek in range(0, nchar_adjusted, blocksize): 

                    for taxon in undelete: 

                        fh.write(safename(taxon, mrbayes=mrbayes).ljust(namelength+1)) 

                        fh.write(cropped_matrix[taxon][seek:seek+blocksize]+'\n') 

                    fh.write('\n') 

            else: 

                for taxon in undelete: 

                    if blocksize<nchar_adjusted: 

                        fh.write(safename(taxon, mrbayes=mrbayes)+'\n') 

                    else: 

                        fh.write(safename(taxon, mrbayes=mrbayes).ljust(namelength+1)) 

                    taxon_seq = cropped_matrix[taxon] 

                    for seek in range(0, nchar_adjusted, blocksize): 

                        fh.write(taxon_seq[seek:seek+blocksize]+'\n') 

                    del taxon_seq 

            fh.write(';\nend;\n') 

            if append_sets: 

                if codons_block: 

                    fh.write(self.append_sets(exclude=exclude, delete=delete, mrbayes=mrbayes, include_codons=False)) 

                    fh.write(self.append_sets(exclude=exclude, delete=delete, mrbayes=mrbayes, codons_only=True)) 

                else: 

                    fh.write(self.append_sets(exclude=exclude, delete=delete, mrbayes=mrbayes)) 

        return filename 

 

    def append_sets(self, exclude=[], delete=[], mrbayes=False, include_codons=True, codons_only=False): 

        """Returns a sets block.""" 

        if not self.charsets and not self.taxsets and not self.charpartitions: 

            return '' 

        if codons_only: 

            setsb = ['\nbegin codons'] 

        else: 

            setsb = ['\nbegin sets'] 

        # - now if characters have been excluded, the character sets need to be adjusted, 

        #   so that they still point to the right character positions 

        # calculate a list of offsets: for each deleted character, the following character position 

        # in the new file will have an additional offset of -1 

        offset = 0 

        offlist = [] 

        for c in range(self.nchar): 

            if c in exclude: 

                offset += 1 

                offlist.append(-1)  # dummy value as these character positions are excluded 

            else: 

                offlist.append(c-offset) 

        # now adjust each of the character sets 

        if not codons_only: 

            for n, ns in self.charsets.items(): 

                cset = [offlist[c] for c in ns if c not in exclude] 

                if cset: 

                    setsb.append('charset %s = %s' % (safename(n), _compact4nexus(cset))) 

            for n, s in self.taxsets.items(): 

                tset = [safename(t, mrbayes=mrbayes) for t in s if t not in delete] 

                if tset: 

                    setsb.append('taxset %s = %s' % (safename(n), ' '.join(tset))) 

        for n, p in self.charpartitions.items(): 

            if not include_codons and n == CODONPOSITIONS: 

                continue 

            elif codons_only and n != CODONPOSITIONS: 

                continue 

            # as characters have been excluded, the partitions must be adjusted 

            # if a partition is empty, it will be omitted from the charpartition command 

            # (although paup allows charpartition part=t1:,t2:,t3:1-100) 

            names = _sort_keys_by_values(p) 

            newpartition = {} 

            for sn in names: 

                nsp = [offlist[c] for c in p[sn] if c not in exclude] 

                if nsp: 

                    newpartition[sn] = nsp 

            if newpartition: 

                if include_codons and n == CODONPOSITIONS: 

                    command = 'codonposset' 

                else: 

                    command = 'charpartition' 

                setsb.append('%s %s = %s' % (command, safename(n), 

                                             ', '.join('%s: %s' % (sn, _compact4nexus(newpartition[sn])) 

                                                       for sn in names if sn in newpartition))) 

        # now write charpartititions, much easier than charpartitions 

        for n, p in self.taxpartitions.items(): 

            names = _sort_keys_by_values(p) 

            newpartition = {} 

            for sn in names: 

                nsp = [t for t in p[sn] if t not in delete] 

                if nsp: 

                    newpartition[sn]=nsp 

            if newpartition: 

                setsb.append('taxpartition %s = %s' % (safename(n), 

                             ', '.join('%s: %s' % (safename(sn), 

                                                   ' '.join(safename(x) for x in newpartition[sn])) 

                                       for sn in names if sn in newpartition))) 

        # add 'end' and return everything 

        setsb.append('end;\n') 

        if len(setsb) == 2: # begin and end only 

            return '' 

        else: 

            return ';\n'.join(setsb) 

 

    def export_fasta(self, filename=None, width=70): 

        """Writes matrix into a fasta file.""" 

        if not filename: 

            if '.' in self.filename and self.filename.split('.')[-1].lower() in ['paup', 'nexus', 'nex', 'dat']: 

                filename = '.'.join(self.filename.split('.')[:-1])+'.fas' 

            else: 

                filename = self.filename+'.fas' 

        with open(filename, 'w') as fh: 

            for taxon in self.taxlabels: 

                fh.write('>' + safename(taxon) + '\n') 

                for i in range(0, len(str(self.matrix[taxon])), width): 

                    fh.write(str(self.matrix[taxon])[i:i+width] + '\n') 

        return filename 

 

    def export_phylip(self, filename=None): 

        """Writes matrix into a PHYLIP file. 

 

        Note that this writes a relaxed PHYLIP format file, where the names 

        are not truncated, nor checked for invalid characters.""" 

        if not filename: 

            if '.' in self.filename and self.filename.split('.')[-1].lower() in ['paup', 'nexus', 'nex', 'dat']: 

                filename = '.'.join(self.filename.split('.')[:-1])+'.phy' 

            else: 

                filename = self.filename+'.phy' 

        with open(filename, 'w') as fh: 

            fh.write('%d %d\n' % (self.ntax, self.nchar)) 

            for taxon in self.taxlabels: 

                fh.write('%s %s\n' % (safename(taxon), str(self.matrix[taxon]))) 

        return filename 

 

    def constant(self, matrix=None, delete=[], exclude=[]): 

        """Return a list with all constant characters.""" 

        if not matrix: 

            matrix = self.matrix 

        undelete = [t for t in self.taxlabels if t in matrix and t not in delete] 

        if not undelete: 

            return None 

        elif len(undelete) == 1: 

            return [x for x in range(len(matrix[undelete[0]])) if x not in exclude] 

        # get the first sequence and expand all ambiguous values 

        constant = [(x, self.ambiguous_values.get(n.upper(), n.upper())) for 

                    x, n in enumerate(str(matrix[undelete[0]])) if x not in exclude] 

 

        for taxon in undelete[1:]: 

            newconstant = [] 

            for site in constant: 

                #print '%d (paup=%d)' % (site[0],site[0]+1), 

                seqsite = matrix[taxon][site[0]].upper() 

                #print seqsite,'checked against',site[1],'\t', 

                if seqsite == self.missing \ 

                or (seqsite == self.gap and self.options['gapmode'].lower() == 'missing') \ 

                or seqsite == site[1]: 

                    # missing or same as before  -> ok 

                    newconstant.append(site) 

                elif seqsite in site[1] \ 

                or site[1] == self.missing \ 

                or (self.options['gapmode'].lower() == 'missing' and site[1] == self.gap): 

                    # subset of an ambig or only missing in previous -> take subset 

                    newconstant.append((site[0], self.ambiguous_values.get(seqsite, seqsite))) 

                elif seqsite in self.ambiguous_values: 

                    # is it an ambig: check the intersection with prev. values 

                    intersect = set(self.ambiguous_values[seqsite]).intersection(set(site[1])) 

                    if intersect: 

                        newconstant.append((site[0], ''.join(intersect))) 

                    #    print 'ok' 

                    #else: 

                    #    print 'failed' 

                #else: 

                #    print 'failed' 

            constant = newconstant 

        cpos = [s[0] for s in constant] 

        return cpos 

 

    def cstatus(self, site, delete=[], narrow=True): 

        """Summarize character. 

 

        narrow=True:  paup-mode (a c ? --> ac; ? ? ? --> ?) 

        narrow=false:           (a c ? --> a c g t -; ? ? ? --> a c g t -) 

        """ 

        undelete = [t for t in self.taxlabels if t not in delete] 

        if not undelete: 

            return None 

        cstatus = [] 

        for t in undelete: 

            c = self.matrix[t][site].upper() 

            if self.options.get('gapmode') == 'missing' and c == self.gap: 

                c = self.missing 

            if narrow and c == self.missing: 

                if c not in cstatus: 

                    cstatus.append(c) 

            else: 

                cstatus.extend(b for b in self.ambiguous_values[c] if b not in cstatus) 

        if self.missing in cstatus and narrow and len(cstatus)>1: 

            cstatus = [c for c in cstatus if c != self.missing] 

        cstatus.sort() 

        return cstatus 

 

    def weighted_stepmatrix(self, name='your_name_here', exclude=[], delete=[]): 

        """Calculates a stepmatrix for weighted parsimony. 

 

        See Wheeler (1990), Cladistics 6:269-275 and 

        Felsenstein (1981), Biol. J. Linn. Soc. 16:183-196 

        """ 

        m = StepMatrix(self.unambiguous_letters, self.gap) 

        for site in [s for s in range(self.nchar) if s not in exclude]: 

            cstatus = self.cstatus(site, delete) 

            for i, b1 in enumerate(cstatus[:-1]): 

                for b2 in cstatus[i+1:]: 

                    m.add(b1.upper(), b2.upper(), 1) 

        return m.transformation().weighting().smprint(name=name) 

 

    def crop_matrix(self, matrix=None, delete=[], exclude=[]): 

        """Return a matrix without deleted taxa and excluded characters.""" 

        if not matrix: 

            matrix = self.matrix 

        if [t for t in delete if not self._check_taxlabels(t)]: 

            raise NexusError('Unknown taxa: %s' 

                             % ', '.join(set(delete).difference(self.taxlabels))) 

        if exclude != []: 

            undelete = [t for t in self.taxlabels if t in matrix and t not in delete] 

            if not undelete: 

                return {} 

            m = [str(matrix[k]) for k in undelete] 

            sitesm = [s for i, s in enumerate(zip(*m)) if i not in exclude] 

            if sitesm == []: 

                return dict((t, Seq('', self.alphabet)) for t in undelete) 

            else: 

                m = [Seq(s, self.alphabet) for s in (''.join(x) for x in zip(*sitesm))] 

                return dict(zip(undelete, m)) 

        else: 

            return dict((t, matrix[t]) for t in self.taxlabels if t in matrix and t not in delete) 

 

    def bootstrap(self, matrix=None, delete=[], exclude=[]): 

        """Return a bootstrapped matrix.""" 

        if not matrix: 

            matrix = self.matrix 

        seqobjects = isinstance(matrix[list(matrix.keys())[0]], Seq) # remember if Seq objects 

        cm = self.crop_matrix(delete=delete, exclude=exclude)       # crop data out 

        if not cm:                                                  # everything deleted? 

            return {} 

        elif not cm[list(cm.keys())[0]]:                            # everything excluded? 

            return cm 

        undelete = [t for t in self.taxlabels if t in cm] 

        if seqobjects: 

            sitesm = list(zip(*[str(cm[t]) for t in undelete])) 

            alphabet = matrix[list(matrix.keys())[0]].alphabet 

        else: 

            sitesm = list(zip(*[cm[t] for t in undelete])) 

        bootstrapsitesm = [sitesm[random.randint(0, len(sitesm)-1)] for i in range(len(sitesm))] 

        bootstrapseqs = [''.join(x) for x in zip(*bootstrapsitesm)] 

        if seqobjects: 

            bootstrapseqs = [Seq(s, alphabet) for s in bootstrapseqs] 

        return dict(zip(undelete, bootstrapseqs)) 

 

    def add_sequence(self, name, sequence): 

        """Adds a sequence (string) to the matrix.""" 

 

        if not name: 

            raise NexusError('New sequence must have a name') 

 

        diff = self.nchar-len(sequence) 

        if diff < 0: 

            self.insert_gap(self.nchar, -diff) 

        elif diff > 0: 

            sequence += self.missing*diff 

 

        if name in self.taxlabels: 

            unique_name = _unique_label(self.taxlabels, name) 

            #print "WARNING: Sequence name %s is already present. Sequence was added as %s." % (name,unique_name) 

        else: 

            unique_name = name 

 

        assert unique_name not in self.matrix, "ERROR. There is a discrepancy between taxlabels and matrix keys. Report this as a bug." 

 

        self.matrix[unique_name] = Seq(sequence, self.alphabet) 

        self.ntax += 1 

        self.taxlabels.append(unique_name) 

        self.unaltered_taxlabels.append(name) 

 

    def insert_gap(self, pos, n=1, leftgreedy=False): 

        """Add a gap into the matrix and adjust charsets and partitions. 

 

        pos=0: first position 

        pos=nchar: last position 

        """ 

 

        def _adjust(set, x, d, leftgreedy=False): 

            """Adjusts character sets if gaps are inserted, taking care of 

            new gaps within a coherent character set.""" 

            # if 3 gaps are inserted at pos. 9 in a set that looks like 1 2 3  8 9 10 11 13 14 15 

            # then the adjusted set will be 1 2 3  8 9 10 11 12 13 14 15 16 17 18 

            # but inserting into position 8 it will stay like 1 2 3 11 12 13 14 15 16 17 18 

            set.sort() 

            addpos = 0 

            for i, c in enumerate(set): 

                if c >= x: 

                    set[i] = c + d 

                # if we add gaps within a group of characters, we want the gap position included in this group 

                if c == x: 

                    if leftgreedy or (i>0 and set[i-1]==c-1): 

                        addpos = i 

            if addpos > 0: 

                set[addpos:addpos] = list(range(x, x+d)) 

            return set 

 

        if pos < 0 or pos > self.nchar: 

            raise NexusError('Illegal gap position: %d' % pos) 

        if n == 0: 

            return 

        sitesm = list(zip(*[str(self.matrix[t]) for t in self.taxlabels])) 

        sitesm[pos:pos] = [['-']*len(self.taxlabels)] * n 

        mapped = [''.join(x) for x in zip(*sitesm)] 

        listed = [(taxon, Seq(mapped[i], self.alphabet)) for i, taxon in enumerate(self.taxlabels)] 

        self.matrix = dict(listed) 

        self.nchar += n 

        # now adjust character sets 

        for i, s in self.charsets.items(): 

            self.charsets[i] = _adjust(s, pos, n, leftgreedy=leftgreedy) 

        for p in self.charpartitions: 

            for sp, s in self.charpartitions[p].items(): 

                self.charpartitions[p][sp] = _adjust(s, pos, n, leftgreedy=leftgreedy) 

        # now adjust character state labels 

        self.charlabels = self._adjust_charlabels(insert=[pos]*n) 

        return self.charlabels 

 

    def _adjust_charlabels(self, exclude=None, insert=None): 

        """Return adjusted indices of self.charlabels if characters are excluded or inserted.""" 

        if exclude and insert: 

            raise NexusError('Can\'t exclude and insert at the same time') 

        if not self.charlabels: 

            return None 

        labels = sorted(self.charlabels) 

        newcharlabels = {} 

        if exclude: 

            exclude.sort() 

            exclude.append(sys.maxsize) 

            excount = 0 

            for c in labels: 

                if not c in exclude: 

                    while c > exclude[excount]: 

                        excount += 1 

                    newcharlabels[c-excount] = self.charlabels[c] 

        elif insert: 

            insert.sort() 

            insert.append(sys.maxsize) 

            icount = 0 

            for c in labels: 

                while c >= insert[icount]: 

                    icount += 1 

                newcharlabels[c+icount] = self.charlabels[c] 

        else: 

            return self.charlabels 

        return newcharlabels 

 

    def invert(self, charlist): 

        """Returns all character indices that are not in charlist.""" 

        return [c for c in range(self.nchar) if c not in charlist] 

 

    def gaponly(self, include_missing=False): 

        """Return gap-only sites.""" 

        gap = set(self.gap) 

        if include_missing: 

            gap.add(self.missing) 

        sitesm = zip(*[str(self.matrix[t]) for t in self.taxlabels]) 

        return [i for i, site in enumerate(sitesm) if set(site).issubset(gap)] 

 

    def terminal_gap_to_missing(self, missing=None, skip_n=True): 

        """Replaces all terminal gaps with missing character. 

 

        Mixtures like ???------??------- are properly resolved.""" 

 

        if not missing: 

            missing = self.missing 

        replace = [self.missing, self.gap] 

        if not skip_n: 

            replace.extend(['n', 'N']) 

        for taxon in self.taxlabels: 

            sequence = str(self.matrix[taxon]) 

            length = len(sequence) 

            start, end = get_start_end(sequence, skiplist=replace) 

            if start == -1 and end == -1: 

                sequence = missing*length 

            else: 

                sequence = sequence[:end+1] + missing*(length-end-1) 

                sequence = start*missing + sequence[start:] 

            assert length==len(sequence), 'Illegal sequence manipulation in Nexus.terminal_gap_to_missing in taxon %s' % taxon 

            self.matrix[taxon] = Seq(sequence, self.alphabet) 

 

 

try: 

    import cnexus 

except ImportError: 

    def _get_command_lines(file_contents): 

        lines = _kill_comments_and_break_lines(file_contents) 

        commandlines = _adjust_lines(lines) 

        return commandlines 

else: 

    def _get_command_lines(file_contents): 

        decommented = cnexus.scanfile(file_contents) 

        #check for unmatched parentheses 

        if decommented == '[' or decommented == ']': 

            raise NexusError('Unmatched %s' % decommented) 

        # cnexus can't return lists, so in analogy we separate 

        # commandlines with chr(7) (a character that shouldn't be part of a 

        # nexus file under normal circumstances) 

        commandlines = _adjust_lines(decommented.split(chr(7))) 

        return commandlines