Bio.Nexus.Nexus.Nexus

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.
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`

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.

Property Details

original_taxon_order

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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