Package Bio :: Package Nexus :: Module Nexus :: Class Nexus
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Type Nexus

object --+
         |
        Nexus


Method Summary
  __init__(self, input)
  add_sequence(self, name, sequence)
Adds a sequence to the matrix.
  append_sets(self, exclude, delete, mrbayes)
Appends a sets block to <filename>.
  bootstrap(self, matrix, delete, exclude)
Return a bootstrapped matrix.
  constant(self, matrix, delete, exclude)
Return a list with all constant characters.
  crop_matrix(self, matrix, delete, exclude)
Return a matrix without deleted taxa and excluded characters.
  cstatus(self, site, delete, narrow)
Summarize character.
  export_fasta(self, filename, width)
Writes matrix into a fasta file: (self, filename=None, width=70).
  gaponly(self, include_missing)
Return gap-only sites.
  get_original_taxon_order(self)
Included for backwards compatibility.
  insert_gap(self, pos, n, leftgreedy)
Add a gap into the matrix and adjust charsets and partitions.
  invert(self, charlist)
Returns all character indices that are not in charlist.
  read(self, input)
Read and parse NEXUS imput (filename, file-handle, string.
  set_original_taxon_order(self, value)
Included for backwards compatibility.
  terminal_gap_to_missing(self, missing, skip_n)
Replaces all terminal gaps with missing character.
  weighted_stepmatrix(self, name, exclude, delete)
Calculates a stepmatrix for weighted parsimony.
  write_nexus_data(self, filename, matrix, exclude, delete, blocksize, interleave, interleave_by_partition, comment, omit_NEXUS, append_sets, mrbayes)
Writes a nexus file with data and sets block.
  write_nexus_data_partitions(self, matrix, filename, blocksize, interleave, exclude, delete, charpartition, comment, mrbayes)
Writes a nexus file for each partition in charpartition.
  _adjust_charlabels(self, exclude, insert)
Return adjusted indices of self.charlabels if characters are excluded or inserted.
  _apply_block_structure(self, title, lines)
  _changeset(self, options)
  _charlabels(self, options)
  _charpartition(self, options)
  _charset(self, options)
  _charstatelabels(self, options)
  _check_taxlabels(self, taxon)
Check for presence of taxon in self.taxlabels.
  _dimensions(self, options)
  _eliminate(self, options)
  _format(self, options)
  _get_indices(self, options, set_type, 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]
  _get_nexus_block(self, file_contents)
Generator for looping through Nexus blocks.
  _matrix(self, options)
  _name_n_vector(self, opts, separator)
Extract name and check that it's not in vector format.
  _options(self, options)
  _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.
  _parse_nexus_block(self, title, contents)
Parse a known Nexus Block
  _resolve(self, identifier, set_type)
Translate identifier in list into character/taxon index.
  _set(self, options)
  _statelabels(self, options)
  _stateset(self, options)
  _taxlabels(self, options)
Get taxon labels.
  _taxpartition(self, options)
  _taxset(self, options)
  _translate(self, options)
  _tree(self, options)
  _treepartition(self, options)
  _treeset(self, options)
  _unknown_nexus_block(self, title, contents)
  _utree(self, options)
Some software (clustalx) uses 'utree' to denote an unrooted tree.
    Inherited from object
  __delattr__(...)
x.__delattr__('name') <==> del x.name
  __getattribute__(...)
x.__getattribute__('name') <==> x.name
  __hash__(x)
x.__hash__() <==> hash(x)
  __new__(T, S, ...)
T.__new__(S, ...) -> a new object with type S, a subtype of T
  __reduce__(...)
helper for pickle
  __reduce_ex__(...)
helper for pickle
  __repr__(x)
x.__repr__() <==> repr(x)
  __setattr__(...)
x.__setattr__('name', value) <==> x.name = value
  __str__(x)
x.__str__() <==> str(x)

Property Summary
  original_taxon_order: Included for backwards compatibility.

Class Variable Summary
list __slots__ = ['original_taxon_order', '__dict__']

Method Details

add_sequence(self, name, sequence)

Adds a sequence to the matrix.

append_sets(self, exclude=[], delete=[], mrbayes=False)

Appends a sets block to <filename>.

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

Return a bootstrapped matrix.

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

Return a list with all constant characters.

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

Return a matrix without deleted taxa and excluded characters.

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 -)

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

Writes matrix into a fasta file: (self, filename=None, width=70).

gaponly(self, include_missing=False)

Return gap-only sites.

get_original_taxon_order(self)

Included for backwards compatibility.

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

invert(self, charlist)

Returns all character indices that are not in charlist.

read(self, input)

Read and parse NEXUS imput (filename, file-handle, string.

set_original_taxon_order(self, value)

Included for backwards compatibility.

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

Replaces all terminal gaps with missing character.

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

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

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.

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.

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

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

_check_taxlabels(self, taxon)

Check for presence of taxon in self.taxlabels.

_get_indices(self, options, set_type='chars', 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]

_get_nexus_block(self, file_contents)

Generator for looping through Nexus blocks.

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

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

_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).

_parse_nexus_block(self, title, contents)

Parse a known Nexus Block

_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

_taxlabels(self, options)

Get taxon labels.

_utree(self, options)

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

Property Details

original_taxon_order

Included for backwards compatibility.
Get Method:
get_original_taxon_order(self)
Set Method:
set_original_taxon_order(self, value)

Class Variable Details

__slots__

Type:
list
Value:
['original_taxon_order', '__dict__']                                   

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