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author | davidmurphy |
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date | Sat, 31 Mar 2012 16:07:07 -0400 |
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# Nexus.py - a NEXUS parser # # Copyright 2005 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@duke.edu # """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 Authors: Frank Kauff and Cymon J. Cox """ import os,sys, math, random, copy import sets # --- Changes from Bio.Nexus --- # Renamed Nexus.py to __init__.py. Helps with api documentation. # One further change in file, tagged with 'GEC' #from Bio.Alphabet import IUPAC #from Bio.Data import IUPACData #from Bio.Seq import Seq from corebio.seq import Seq, Alphabet, protein_alphabet import corebio.data as data from corebio.utils import Struct IUPACData = Struct( ambiguous_dna_letters = data.dna_extended_letters, ambiguous_rna_letters = data.rna_extended_letters, ambiguous_dna_values = data.dna_ambiguity, ambiguous_rna_values = data.rna_ambiguity, protein_letters = data.amino_acid_letters, unambiguous_dna_letters = data.dna_letters, unambiguous_rna_letters = data.rna_letters, ) IUPAC = Struct( ambiguous_dna = Alphabet(IUPACData.ambiguous_dna_letters+'-?'), ambiguous_rna = Alphabet(IUPACData.ambiguous_rna_letters+'-?'), protein = protein_alphabet #Alphabet(IUPACData.protein_letters+'-?') ) # End Changes from Trees import Tree,NodeData C = False #try: # import cnexus #except ImportError: # C=False #else: # C=True INTERLEAVE=70 SPECIAL_COMMANDS=['charstatelabels','charlabels','taxlabels', 'taxset', 'charset','charpartition','taxpartition',\ 'matrix','tree', 'utree','translate'] KNOWN_NEXUS_BLOCKS = ['trees','data', 'characters', 'taxa', 'sets'] 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' class NexusError(Exception): pass class CharBuffer: """Helps reading NEXUS-words and characters from a buffer.""" 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 def next_nonwhitespace(self): while True: p=self.next() 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, dealing 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=True elif first in PUNCTUATION: # if it's punctuation, return immediately return first while True: c=self.peek() if c=="'": # a quote? word.append(self.next()) # store quote if self.peek()=="'": # double quote skip=self.next() # skip second quote elif quoted: # second single quote ends word break elif quoted: word.append(self.next()) # 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(self.next()) # standard character return ''.join(word) def rest(self): """Return the rest of the string without parsing.""" return ''.join(self.buffer) class StepMatrix: """Calculate a stepmatrix for weighted parsimony. See Wheeler (1990), Cladistics 6:269-275. """ def __init__(self,symbols,gap): self.data={} self.symbols=[s for s in symbols] self.symbols.sort() 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 mrbayes. """ if mrbayes: safe=name.replace(' ','_') safe=''.join([c for c in safe if c in MRBAYESSAFE]) else: safe=name.replace("'","''") if sets.Set(safe).intersection(sets.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 (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 return start,end def _sort_keys_by_values(p): """Returns a sorted list of keys of p sorted by values of p.""" startpos=[(p[pn],pn) for pn in p if p[pn]] startpos.sort() return zip(*startpos)[1] def _make_unique(l): """Check that all values in list are unique and return a pruned and sorted list.""" l=list(sets.Set(l)) l.sort() return l def _seqmatrix2strmatrix(matrix): """Converts a Seq-object matrix to a plain sequence-string matrix.""" return dict([(t,matrix[t].tostring()) 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=list(sets.Set(orig_list)) orig_list.sort() 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(sets.Set([n[1].datatype for n in matrices]))>1) if mixed_datatypes: combined.datatype='None' # dealing with mixed matrices is application specific. You take care of that yourself! # 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: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(m.matrix[t].tostring().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(m.matrix[t].tostring().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={} combined.taxsets.update(dict([('%s.%s' % (n,tn),ts) for tn,ts in m.taxsets.items()])) # update taxon sets combined.charpartitions['combined'][n]=range(combined.nchar,combined.nchar+m.nchar) # update new charpartition # 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) 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=CharBuffer(text) newtext=[] newline=[] quotelevel='' speciallevel=False commlevel=0 while True: #plain=contents.next_until(["'",'"','[',']','\n',';']) # search for next special character #if not plain: # newline.append(contents.rest) # not found, just add the rest # break #newline.append(plain) # add intermediate text t=contents.next() # and get special character 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 contents.peek() 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=[x for x in seq[opening+1:closing]] ambig.sort() ambig=''.join(ambig) 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: """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: """Represent a NEXUS block with block name and list of commandlines .""" def __init__(self,title=None): self.title=title self.commandlines=[] class Nexus(object): __slots__=['original_taxon_order','__dict__'] def __init__(self, input=None): self.ntax=0 # number of taxa self.nchar=0 # number of characters 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 # some defaults self.options['gapmode']='missing' if input: self.read(input) def get_original_taxon_order(self): """Included for backwards compatibility.""" return self.taxlabels def set_original_taxon_order(self,value): """Included for backwards compatibility.""" self.taxlabels=value original_taxon_order=property(get_original_taxon_order,set_original_taxon_order) def read(self,input): """Read and parse NEXUS imput (filename, file-handle, string.""" # 1. Assume we have the name of a file in the execution dir # Note we need to add parsing of the path to dir/filename try: file_contents = open(os.path.expanduser(input),'rU').read() self.filename=input except (TypeError,IOError,AttributeError): #2 Assume we have a string from a fh.read() #if isinstance(input, str): # file_contents = input # self.filename='input_string' #3 Assume we have a file object if hasattr(input,'read'): # file objects or StringIO objects file_contents=input.read() # GEC : Change next line so that StringIO objects work #if input.name: if hasattr(input, 'name'): self.filename=input.name else: self.filename='Unknown_nexus_file' else: print input.strip()[:6] raise NexusError, 'Unrecognized input: %s ...' % input[:100] if C: 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 shoudn't be part of a nexus file under normal circumstances) commandlines=_adjust_lines(decommented.split(chr(7))) else: commandlines=_adjust_lines(_kill_comments_and_break_lines(file_contents)) # get rid of stupid 'NEXUS token' try: if commandlines[0][:6].upper()=='#NEXUS': commandlines[0]=commandlines[0][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 1: try: title, contents = nexus_block_gen.next() 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 """ # 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 raise NexusError, 'Unknown command: %s ' % line.command def _dimensions(self,options): if options.has_key('ntax'): self.ntax=eval(options['ntax']) if options.has_key('nchar'): 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 options.has_key('respectcase'): self.respectcase=True # adjust symbols to for respectcase if options.has_key('symbols'): 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(sets.Set(self.symbols)) if options.has_key('datatype'): self.datatype=options['datatype'].lower() if self.datatype=='dna' or self.datatype=='nucleotide': self.alphabet=IUPAC.ambiguous_dna self.ambiguous_values=IUPACData.ambiguous_dna_values self.unambiguous_letters=IUPACData.unambiguous_dna_letters elif self.datatype=='rna': self.alphabet=IUPAC.ambiguous_rna self.ambiguous_values=IUPACData.ambiguous_rna_values self.unambiguous_letters=IUPACData.unambiguous_rna_letters elif self.datatype=='protein': self.alphabet=IUPAC.protein 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.keys())+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=[c for c in k] key.sort() 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 options.has_key('missing'): self.missing=options['missing'][0] if options.has_key('gap'): self.gap=options['gap'][0] if options.has_key('equate'): self.equate=options['equate'] if options.has_key('matchchar'): self.matchchar=options['matchchar'][0] if options.has_key('labels'): self.labels=options['labels'] if options.has_key('transpose'): raise NexusError, 'TRANSPOSE is not supported!' self.transpose=True if options.has_key('interleave'): if options['interleave']==None or options['interleave'].lower()=='yes': self.interleave=True if options.has_key('tokens'): self.tokens=True if options.has_key('notokens'): 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.""" 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: try: # 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 except NexusError: raise except: raise NexusError,'Format error 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!' taxlabels_present=(self.taxlabels!=[]) self.matrix={} taxcount=0 block_interleave=0 #eliminate empty lines and leading/trailing whitespace lines=[l.strip() for l in options.split('\n') if l.strip()<>''] lineiter=iter(lines) while 1: try: l=lineiter.next() 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 block_interleave=1 #get taxon name and sequence linechars=CharBuffer(l) id=quotestrip(linechars.next_word()) l=linechars.rest().strip() if taxlabels_present and not self._check_taxlabels(id): raise NexusError,'Taxon '+id+' not found in taxlabels.' chars='' if self.interleave: #interleaved matrix #print 'In interleave' if l: chars=''.join(l.split()) else: chars=''.join(lineiter.next().split()) else: #non-interleaved matrix chars=''.join(l.split()) while len(chars)<self.nchar: l=lineiter.next() 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 1: p=iupac_seq.tostring().find(self.matchchar) if p==-1: break iupac_seq=Seq(iupac_seq.tostring()[:p]+refseq[p]+iupac_seq.tostring()[p+1:],self.alphabet) #check for invalid characters for i,c in enumerate(iupac_seq.tostring()): if c not in self.valid_characters and c!=self.gap and c!=self.missing: raise NexusError, 'Taxon %s: Illegal character %s in line: %s (check dimensions / interleaving)'\ % (id,c,l[i-10:i+10]) #add sequence to matrix if block_interleave==0: while self.matrix.has_key(id): if id.split('.')[-1].startswith('copy'): id='.'.join(id.split('.')[:-1])+'.copy'+str(eval('0'+id.split('.')[-1][4:])+1) else: id+='.copy' #raise NexusError, id+' already in matrix!\nError in: '+l self.matrix[id]=iupac_seq # add taxon name only if taxlabels is not alredy present if not taxlabels_present: self.taxlabels.append(id) else: 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.' % id #check all sequences for length according to nchar for taxon in self.matrix: if len(self.matrix[taxon])!=self.nchar: raise NexusError,'Nchar ('+str(self.nchar)+') does not match data for taxon '+taxon 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) 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=opts.next() if symbol!='&': raise NexusError,'Illegal special comment [%s...] in tree description: %s' % (symbol, options[:50]) special=opts.next() value=opts.next_until(']') closing=opts.next() 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 substitue %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=opts.next() 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 _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=opts.next() 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 '1 2 3 - 5 dog cat 10- 20 \\ 3' --> [0,1,2,3,4,'dog','cat',10,13,16,19] """ 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() 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' % (options) elif qualifier.lower()!='standard': raise NexusError, 'Unknown qualifier %s in line %s' % (qualifier,options) 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: [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 erros, 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 type(start)==list or type(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 type(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 translaterd into their indices (if plain character indentifiers), 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): """ Writes a nexus file with data and sets block. 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. """ 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, 'Unknwon taxa: %s' % ', '.join(sets.Set(delete).difference(sets.Set(self.taxlabels))) if interleave_by_partition: if not interleave_by_partition in self.charpartitions: raise NexusError, 'Unknown partition: '+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 if isinstance(filename,str): try: fh=open(filename,'w') except IOError: raise NexusError, 'Could not open %s for writing.' % filename elif isinstance(filename,file): fh=filename 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=newcharlabels.keys() clkeys.sort() 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)) for seek in range(0,nchar_adjusted,blocksize): fh.write(cropped_matrix[taxon][seek:seek+blocksize]+'\n') fh.write(';\nend;\n') if append_sets: fh.write(self.append_sets(exclude=exclude,delete=delete,mrbayes=mrbayes)) fh.close() return filename def append_sets(self,exclude=[],delete=[],mrbayes=False): """Appends a sets block to <filename>.""" if not self.charsets and not self.taxsets and not self.charpartitions: return '' sets=['\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 for n,ns in self.charsets.items(): cset=[offlist[c] for c in ns if c not in exclude] if cset: sets.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: sets.append('taxset %s = %s' % (safename(n),' '.join(tset))) for n,p in self.charpartitions.items(): # 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: sets.append('charpartition %s = %s' % (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: sets.append('taxpartition %s = %s' % (safename(n),\ ', '.join(['%s: %s' % (safename(sn),' '.join(map(safename,newpartition[sn]))) for sn in names if sn in newpartition]))) # add 'end' and return everything sets.append('end;\n') return ';\n'.join(sets) f.close() def export_fasta(self, filename=None, width=70): """Writes matrix into a fasta file: (self, filename=None, width=70).""" if not filename: if '.' in filename and self.filename.split('.')[-1].lower() in ['paup','nexus','nex','dat']: filename='.'.join(self.filename.split('.')[:-1])+'.fas' else: filename=self.filename+'.fas' fh=open(filename,'w') for taxon in self.taxlabels: fh.write('>'+safename(taxon)+'\n') for i in range(0, len(self.matrix[taxon].tostring()), width): fh.write(self.matrix[taxon].tostring()[i:i+width] + '\n') fh.close() 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(matrix[undelete[0]].tostring()) 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=sets.Set(self.ambiguous_values[seqsite]).intersection(sets.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 constant # return [x[0] for x in constant] 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, 'Unknwon taxa: %s' % ', '.join(sets.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=[matrix[k].tostring() for k in undelete] zipped_m=zip(*m) sitesm=[s for i,s in enumerate(zipped_m) if i not in exclude] if sitesm==[]: return dict([(t,Seq('',self.alphabet)) for t in undelete]) else: zipped_sitesm=zip(*sitesm) m=[Seq(s,self.alphabet) for s in map(''.join,zipped_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[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 len(cm[cm.keys()[0]])==0: # everything excluded? return cm undelete=[t for t in self.taxlabels if t in cm] if seqobjects: sitesm=zip(*[cm[t].tostring() for t in undelete]) alphabet=matrix[matrix.keys()[0]].alphabet else: sitesm=zip(*[cm[t] for t in undelete]) bootstrapsitesm=[sitesm[random.randint(0,len(sitesm)-1)] for i in range(len(sitesm))] bootstrapseqs=map(''.join,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 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 self.matrix[name]=Seq(sequence,self.alphabet) self.ntax+=1 self.taxlabels.append(name) #taxlabels? 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 chartacter 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]=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=zip(*[self.matrix[t].tostring() for t in self.taxlabels]) sitesm[pos:pos]=[['-']*len(self.taxlabels)]*n # #self.matrix=dict([(taxon,Seq(map(''.join,zip(*sitesm))[i],self.alphabet)) for\ # i,taxon in enumerate(self.taxlabels)]) zipped=zip(*sitesm) mapped=map(''.join,zipped) 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=self.charlabels.keys() labels.sort() newcharlabels={} if exclude: exclude.sort() exclude.append(sys.maxint) 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.maxint) 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=sets.Set(self.gap) if include_missing: gap.add(self.missing) sitesm=zip(*[self.matrix[t].tostring() for t in self.taxlabels]) gaponly=[i for i,site in enumerate(sitesm) if sets.Set(site).issubset(gap)] return gaponly 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=self.matrix[taxon].tostring() length=len(sequence) start,end=get_start_end(sequence,skiplist=replace) sequence=sequence[:end+1]+missing*(length-end-1) sequence=start*missing+sequence[start:] assert length==len(sequence), 'Illegal sequence manipulation in Nexus.termial_gap_to_missing in taxon %s' % taxon self.matrix[taxon]=Seq(sequence,self.alphabet)