PHYLIP

Description

Reading

Schema-Specific Keyword Arguments

Supported Methods

DnaCharacterMatrix.get

(method reference)

d = dendropy.DnaCharacterMatrix.get(
        path="data.phylip",
        schema="phylip",
        label=None,
        taxon_namespace=None,
        matrix_offset=None,
        strict=False,
        interleaved=False,
        multispace_delimiter=False,
        underscore_to_spaces=False,
        ignore_invalid_chars=False,
        ignore_unrecognized_keyword_arguments=False,
        )

RnaCharacterMatrix.get

(method reference)

d = dendropy.RnaCharacterMatrix.get(
        path="data.phylip",
        schema="phylip",
        label=None,
        taxon_namespace=None,
        matrix_offset=None,
        strict=False,
        interleaved=False,
        multispace_delimiter=False,
        underscore_to_spaces=False,
        ignore_invalid_chars=False,
        ignore_unrecognized_keyword_arguments=False,
        )

ProteinCharacterMatrix.get

(method reference)

d = dendropy.ProteinCharacterMatrix.get(
        path="data.phylip",
        schema="phylip",
        label=None,
        taxon_namespace=None,
        matrix_offset=None,
        strict=False,
        interleaved=False,
        multispace_delimiter=False,
        underscore_to_spaces=False,
        ignore_invalid_chars=False,
        ignore_unrecognized_keyword_arguments=False,
        )

RestrictionSitesCharacterMatrix.get

(method reference)

d = dendropy.RestrictionSitesCharacterMatrix.get(
        path="data.phylip",
        schema="phylip",
        label=None,
        taxon_namespace=None,
        matrix_offset=None,
        strict=False,
        interleaved=False,
        multispace_delimiter=False,
        underscore_to_spaces=False,
        ignore_invalid_chars=False,
        ignore_unrecognized_keyword_arguments=False,
        )

InfiniteSitesCharacterMatrix.get

(method reference)

d = dendropy.InfiniteSitesCharacterMatrix.get(
        path="data.phylip",
        schema="phylip",
        label=None,
        taxon_namespace=None,
        matrix_offset=None,
        strict=False,
        interleaved=False,
        multispace_delimiter=False,
        underscore_to_spaces=False,
        ignore_invalid_chars=False,
        ignore_unrecognized_keyword_arguments=False,
        )

StandardCharacterMatrix.get

(method reference)

d = dendropy.StandardCharacterMatrix.get(
        path="data.phylip",
        schema="phylip",
        label=None,
        taxon_namespace=None,
        matrix_offset=None,
        strict=False,
        interleaved=False,
        multispace_delimiter=False,
        underscore_to_spaces=False,
        ignore_invalid_chars=False,
        ignore_unrecognized_keyword_arguments=False,
        default_state_alphabet=None,
        )

d = dendropy.StandardCharacterMatrix.get(
        path="data.phylip",
        schema="phylip",
        label=None,
        taxon_namespace=None,
        matrix_offset=None,
        strict=False,
        interleaved=False,
        multispace_delimiter=False,
        underscore_to_spaces=False,
        ignore_invalid_chars=False,
        ignore_unrecognized_keyword_arguments=False,
        default_state_alphabet=dendropy.new_standard_state_alphabet("0123456789"),
        )

DataSet.get

(method reference)

Note that the type of data needs to be specified using the data_type keyword argument.

d = dendropy.DataSet.get(
        path="data.phylip",
        schema="phylip",
        label=None,
        taxon_namespace=None,
        strict=False,
        interleaved=False,
        multispace_delimiter=False,
        underscore_to_spaces=False,
        ignore_invalid_chars=False,
        ignore_unrecognized_keyword_arguments=False,
        data_type="dna",
        )

d = dendropy.DataSet.get(
        path="data.phylip",
        schema="phylip",
        label=None,
        taxon_namespace=None,
        strict=False,
        interleaved=False,
        multispace_delimiter=False,
        underscore_to_spaces=False,
        ignore_invalid_chars=False,
        ignore_unrecognized_keyword_arguments=False,
        data_type="dna",
        )

d = dendropy.DataSet.get(
        path="data.phylip",
        schema="phylip",
        label=None,
        taxon_namespace=None,
        strict=False,
        interleaved=False,
        multispace_delimiter=False,
        underscore_to_spaces=False,
        ignore_invalid_chars=False,
        ignore_unrecognized_keyword_arguments=False,
        data_type="standard",
        )

d = dendropy.DataSet.get(
        path="data.phylip",
        schema="phylip",
        label=None,
        taxon_namespace=None,
        strict=False,
        interleaved=False,
        multispace_delimiter=False,
        underscore_to_spaces=False,
        ignore_invalid_chars=False,
        ignore_unrecognized_keyword_arguments=False,
        data_type="standard",
        default_state_alphabet=dendropy.new_standard_state_alphabet("01")
        )

DataSet.read

(method reference)

Note that the type of data needs to be specified using the data_type keyword argument.

d = dendropy.DataSet()
d.read(
        path="data.phylip",
        schema="phylip",
        label=None,
        taxon_namespace=None,
        strict=False,
        interleaved=False,
        multispace_delimiter=False,
        underscore_to_spaces=False,
        ignore_invalid_chars=False,
        ignore_unrecognized_keyword_arguments=False,
        data_type="dna",
        )

d = dendropy.DataSet()
d.read(
        path="data.phylip",
        schema="phylip",
        label=None,
        taxon_namespace=None,
        strict=False,
        interleaved=False,
        multispace_delimiter=False,
        underscore_to_spaces=False,
        ignore_invalid_chars=False,
        ignore_unrecognized_keyword_arguments=False,
        data_type="protein",
        )

d = dendropy.DataSet()
d.read(
        path="data.phylip",
        schema="phylip",
        label=None,
        taxon_namespace=None,
        strict=False,
        interleaved=False,
        multispace_delimiter=False,
        underscore_to_spaces=False,
        ignore_invalid_chars=False,
        ignore_unrecognized_keyword_arguments=False,
        data_type="standard",
        )

d = dendropy.DataSet()
d.read(
        path="data.phylip",
        schema="phylip",
        label=None,
        taxon_namespace=None,
        strict=False,
        interleaved=False,
        multispace_delimiter=False,
        underscore_to_spaces=False,
        ignore_invalid_chars=False,
        ignore_unrecognized_keyword_arguments=False,
        data_type="standard",
        default_state_alphabet=dendropy.new_standard_state_alphabet("abc"),
        )

Writing

Schema-Specific Keyword Arguments

Supported Methods

DnaCharacterMatrix.write

(method reference)

d.write(
        path="data.phylip",
        schema="phylip",
        strict=False,
        spaces_to_underscores=False,
        force_unique_taxon_labels=False,
        suppress_missing_taxa=False,
        ignore_unrecognized_keyword_arguments=False,
        )

DnaCharacterMatrix.as_string

(method reference)

s = d.as_string(
        schema="phylip",
        strict=False,
        spaces_to_underscores=False,
        force_unique_taxon_labels=False,
        ignore_unrecognized_keyword_arguments=False,
        )

RnaCharacterMatrix.write

(method reference)

d.write(
        path="data.phylip",
        schema="phylip",
        strict=False,
        spaces_to_underscores=False,
        force_unique_taxon_labels=False,
        suppress_missing_taxa=False,
        ignore_unrecognized_keyword_arguments=False,
        )

RnaCharacterMatrix.as_string

(method reference)

s = d.as_string(
        schema="phylip",
        strict=False,
        spaces_to_underscores=False,
        force_unique_taxon_labels=False,
        ignore_unrecognized_keyword_arguments=False,
        )

ProteinCharacterMatrix.write

(method reference)

d.write(
        path="data.phylip",
        schema="phylip",
        strict=False,
        spaces_to_underscores=False,
        force_unique_taxon_labels=False,
        suppress_missing_taxa=False,
        ignore_unrecognized_keyword_arguments=False,
        )

ProteinCharacterMatrix.as_string

(method reference)

s = d.as_string(
        schema="phylip",
        strict=False,
        spaces_to_underscores=False,
        force_unique_taxon_labels=False,
        ignore_unrecognized_keyword_arguments=False,
        )

RestrictionSitesCharacterMatrix.write

(method reference)

d.write(
        path="data.phylip",
        schema="phylip",
        strict=False,
        spaces_to_underscores=False,
        force_unique_taxon_labels=False,
        suppress_missing_taxa=False,
        ignore_unrecognized_keyword_arguments=False,
        )

RestrictionSitesCharacterMatrix.as_string

(method reference)

s = d.as_string(
        schema="phylip",
        strict=False,
        spaces_to_underscores=False,
        force_unique_taxon_labels=False,
        ignore_unrecognized_keyword_arguments=False,
        )

InfiniteSitesCharacterMatrix.write

(method reference)

d.write(
        path="data.phylip",
        schema="phylip",
        strict=False,
        spaces_to_underscores=False,
        force_unique_taxon_labels=False,
        suppress_missing_taxa=False,
        ignore_unrecognized_keyword_arguments=False,
        )

InfiniteSitesCharacterMatrix.as_string

(method reference)

s = d.as_string(
        schema="phylip",
        strict=False,
        spaces_to_underscores=False,
        force_unique_taxon_labels=False,
        ignore_unrecognized_keyword_arguments=False,
        )

StandardCharacterMatrix.write

(method reference)

d.write(
        path="data.phylip",
        schema="phylip",
        strict=False,
        spaces_to_underscores=False,
        force_unique_taxon_labels=False,
        suppress_missing_taxa=False,
        ignore_unrecognized_keyword_arguments=False,
        )

StandardCharacterMatrix.as_string

(method reference)

s = d.as_string(
        schema="phylip",
        strict=False,
        spaces_to_underscores=False,
        force_unique_taxon_labels=False,
        ignore_unrecognized_keyword_arguments=False,
        )

DataSet.write

(method reference)

d.write(
        path="data.phylip",
        schema="phylip",
        strict=False,
        spaces_to_underscores=False,
        force_unique_taxon_labels=False,
        suppress_missing_taxa=False,
        ignore_unrecognized_keyword_arguments=False,
        )

DataSet.as_string

(method reference)

s = d.as_string(
        schema="phylip",
        strict=False,
        spaces_to_underscores=False,
        force_unique_taxon_labels=False,
        ignore_unrecognized_keyword_arguments=False,
        )