FASTA

Description

• http://en.wikipedia.org/wiki/FASTA_format
• Lipman, DJ; Pearson, WR (1985). “Rapid and sensitive protein similarity searches”. Science 227 (4693): 1435–41. doi:10.1126/science.2983426.

Reading

Schema-Specific Keyword Arguments

• data_type (str) – When reading into a DataSet object, the type of data must be specified: “dna”, “rna”, “protein”, “restriction”, “infinite”, “standard”, or “continuous”.
• default_state_alphabet (|StateAlphabet| instance) – A StateAlphabet object to be used to manage the alphabet of the characters (StandardCharacterMatrix only).

Supported Methods

DnaCharacterMatrix.get

(method reference)

d = dendropy.DnaCharacterMatrix.get(
        path="data.fas",
        schema="fasta",
        label=None,
        taxon_namespace=None,
        matrix_offset=None,
        ignore_unrecognized_keyword_arguments=False,
        )

RnaCharacterMatrix.get

(method reference)

d = dendropy.RnaCharacterMatrix.get(
        path="data.fas",
        schema="fasta",
        label=None,
        taxon_namespace=None,
        matrix_offset=None,
        ignore_unrecognized_keyword_arguments=False,
        )

ProteinCharacterMatrix.get

(method reference)

d = dendropy.ProteinCharacterMatrix.get(
        path="data.fas",
        schema="fasta",
        label=None,
        taxon_namespace=None,
        matrix_offset=None,
        ignore_unrecognized_keyword_arguments=False,
        )

RestrictionSitesCharacterMatrix.get

(method reference)

d = dendropy.RestrictionSitesCharacterMatrix.get(
        path="data.fas",
        schema="fasta",
        label=None,
        taxon_namespace=None,
        matrix_offset=None,
        ignore_unrecognized_keyword_arguments=False,
        )

InfiniteSitesCharacterMatrix.get

(method reference)

d = dendropy.InfiniteSitesCharacterMatrix.get(
        path="data.fas",
        schema="fasta",
        label=None,
        taxon_namespace=None,
        matrix_offset=None,
        ignore_unrecognized_keyword_arguments=False,
        )

StandardCharacterMatrix.get

(method reference)

d = dendropy.StandardCharacterMatrix.get(
        path="data.fas",
        schema="fasta",
        label=None,
        taxon_namespace=None,
        matrix_offset=None,
        ignore_unrecognized_keyword_arguments=False,
        default_state_alphabet=None,
        )

d = dendropy.StandardCharacterMatrix.get(
        path="data.fas",
        schema="fasta",
        label=None,
        taxon_namespace=None,
        matrix_offset=None,
        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.fas",
        schema="fasta",
        label=None,
        taxon_namespace=None,
        ignore_unrecognized_keyword_arguments=False,
        data_type="dna",
        )

d = dendropy.DataSet.get(
        path="data.fas",
        schema="fasta",
        label=None,
        taxon_namespace=None,
        ignore_unrecognized_keyword_arguments=False,
        data_type="dna",
        )

d = dendropy.DataSet.get(
        path="data.fas",
        schema="fasta",
        label=None,
        taxon_namespace=None,
        ignore_unrecognized_keyword_arguments=False,
        data_type="standard",
        )

d = dendropy.DataSet.get(
        path="data.fas",
        schema="fasta",
        label=None,
        taxon_namespace=None,
        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.fas",
        schema="fasta",
        label=None,
        taxon_namespace=None,
        ignore_unrecognized_keyword_arguments=False,
        data_type="dna",
        )

d = dendropy.DataSet()
d.read(
        path="data.fas",
        schema="fasta",
        label=None,
        taxon_namespace=None,
        ignore_unrecognized_keyword_arguments=False,
        data_type="protein",
        )

d = dendropy.DataSet()
d.read(
        path="data.fas",
        schema="fasta",
        label=None,
        taxon_namespace=None,
        ignore_unrecognized_keyword_arguments=False,
        data_type="standard",
        )

d = dendropy.DataSet()
d.read(
        path="data.fas",
        schema="fasta",
        label=None,
        taxon_namespace=None,
        ignore_unrecognized_keyword_arguments=False,
        data_type="standard",
        default_state_alphabet=dendropy.new_standard_state_alphabet("abc"),
        )

Writing

Schema-Specific Keyword Arguments

wrap (boolean, default: |True|) – If False, then sequences are written out as single, unbroken lines. Defaults to True: wraps sequences at 70 colums.

Supported Methods

DnaCharacterMatrix.write

(method reference)

d.write(
        path="data.fas",
        schema="fasta",
        wrap=True,
        ignore_unrecognized_keyword_arguments=False,
        )

DnaCharacterMatrix.as_string

(method reference)

s = d.as_string(
        schema="fasta",
        wrap=True,
        ignore_unrecognized_keyword_arguments=False,
        )

RnaCharacterMatrix.write

(method reference)

d.write(
        path="data.fas",
        schema="fasta",
        wrap=True,
        ignore_unrecognized_keyword_arguments=False,
        )

RnaCharacterMatrix.as_string

(method reference)

s = d.as_string(
        schema="fasta",
        wrap=True,
        ignore_unrecognized_keyword_arguments=False,
        )

ProteinCharacterMatrix.write

(method reference)

d.write(
        path="data.fas",
        schema="fasta",
        wrap=True,
        ignore_unrecognized_keyword_arguments=False,
        )

ProteinCharacterMatrix.as_string

(method reference)

s = d.as_string(
        schema="fasta",
        wrap=True,
        ignore_unrecognized_keyword_arguments=False,
        )

RestrictionSitesCharacterMatrix.write

(method reference)

d.write(
        path="data.fas",
        schema="fasta",
        wrap=True,
        ignore_unrecognized_keyword_arguments=False,
        )

RestrictionSitesCharacterMatrix.as_string

(method reference)

s = d.as_string(
        schema="fasta",
        wrap=True,
        ignore_unrecognized_keyword_arguments=False,
        )

InfiniteSitesCharacterMatrix.write

(method reference)

d.write(
        path="data.fas",
        schema="fasta",
        wrap=True,
        ignore_unrecognized_keyword_arguments=False,
        )

InfiniteSitesCharacterMatrix.as_string

(method reference)

s = d.as_string(
        schema="fasta",
        wrap=True,
        ignore_unrecognized_keyword_arguments=False,
        )

StandardCharacterMatrix.write

(method reference)

d.write(
        path="data.fas",
        schema="fasta",
        wrap=True,
        ignore_unrecognized_keyword_arguments=False,
        )

StandardCharacterMatrix.as_string

(method reference)

s = d.as_string(
        schema="fasta",
        wrap=True,
        ignore_unrecognized_keyword_arguments=False,
        )

DataSet.write

(method reference)

d.write(
        path="data.fas",
        schema="fasta",
        wrap=True,
        ignore_unrecognized_keyword_arguments=False,
        )

DataSet.as_string

(method reference)

s = d.as_string(
        schema="fasta",
        wrap=True,
        ignore_unrecognized_keyword_arguments=False,
        )