class Bio::Fasta
- Bio::Fasta
- Bio::SequenceDB
- Reference
- Object
Overview
Fasta SequenceDB created from a fasta file.
The descriptors of each sequence will be based on the fields separated by '|' as defined in the format. Descriptor names can be provided optionally for further filtering.
Defined in:
sequence/fasta.crConstructors
-
.new(str : String, id_field : Int32 = 0, descriptor_names = nil, sequence_type = Bio::SequenceType::Undefined)
Creates a new Fasta object from a fasta-formatted String.
Class Method Summary
-
.from_file(path, id_field = 0, descriptor_names = nil, sequence_type = Bio::SequenceType::Undefined)
Creates a new Fasta object from a local fasta file.
-
.from_url
TODO implement this method
Instance methods inherited from class Bio::SequenceDB
data : Hash(String, Sequence)
data,
data=(data : Hash(String, Sequence))
data=,
descriptor_names : Array(String) | Nil
descriptor_names,
record(id : String)
record,
records
records,
sequence_type : SequenceType
sequence_type,
to_fasta_str
to_fasta_str
Constructor methods inherited from class Bio::SequenceDB
new(descriptor_names : Nil | Array(String) = nil, sequence_type : Bio::SequenceType = Bio::SequenceType::Undefined)
new
Constructor Detail
def self.new(str : String, id_field : Int32 = 0, descriptor_names = nil, sequence_type = Bio::SequenceType::Undefined)
#
Creates a new Fasta object from a fasta-formatted String. id_field is the univocal identificator of the sequence within the database. descriptor_names can be optionally provided for the fields within the sequence header.
Class Method Detail
def self.from_file(path, id_field = 0, descriptor_names = nil, sequence_type = Bio::SequenceType::Undefined)
#
Creates a new Fasta object from a local fasta file.