API Reference
Public
Internal
GFF3.Reader
— MethodGFF3.Reader(input::IO;
index=nothing,
save_directives::Bool=false,
skip_features::Bool=false,
skip_directives::Bool=true,
skip_comments::Bool=true)
GFF3.Reader(input::AbstractString;
index=:auto,
save_directives::Bool=false,
skip_features::Bool=false,
skip_directives::Bool=true,
skip_comments::Bool=true)
Create a reader for data in GFF3 format.
The first argument specifies the data source. When it is a filepath that ends with .bgz, it is considered to be block compression file format (BGZF) and the function will try to find a tabix index file (<filename>.tbi) and read it if any. See http://www.htslib.org/doc/tabix.html for bgzip and tabix tools.
Arguments
input
: data source (IO
object or filepath)index
: path to a tabix filesave_directives
: flag to save directive records (which can be accessed withGFF3.directives
)skip_features
: flag to skip feature recordsskip_directives
: flag to skip directive recordsskip_comments
: flag to skip comment records
GFF3.Record
— MethodGFF3.Record(str::AbstractString)
Create a GFF3 record object from str
. This function verifies and indexes fields for accessors.
GFF3.Record
— MethodGFF3.Record(data::Vector{UInt8})
Create a GFF3 record object from data
. This function verifies and indexes fields for accessors. Note that the ownership of data
is transferred to a new record object.
GFF3.Record
— MethodGFF3.Record()
Create an unfilled GFF3 record.
GFF3.Writer
— TypeGFF3.Writer(output::IO)
Create a data writer of the GFF3 file format.
Arguments:
output
: data sink
GFF3.attributes
— Methodattributes(record::Record, key::String)::Vector{String}
Get the attributes of record
with key
.
GFF3.attributes
— Methodattributes(record::Record)::Vector{Pair{String,Vector{String}}}
Get the attributes of record
.
GFF3.content
— Methodcontent(record::Record)::String
Get the content of record
. Leading '#' letters are removed.
GFF3.directives
— MethodReturn all directives that preceded the last GFF entry parsed as an array of strings.
Directives at the end of the file can be accessed by calling close(reader)
and then directives(reader)
.
GFF3.featuretype
— Methodfeaturetype(record::Record)::String
Get the type of record
.
GFF3.getfasta
— MethodReturn a FASTA.Reader initialized to parse trailing FASTA data.
Throws an exception if there is no trailing FASTA, which can be checked using hasfasta
.
GFF3.hasfasta
— MethodReturn true if the GFF3 stream is at its end and there is trailing FASTA data.
GFF3.iscomment
— Methodiscomment(record::Record)::Bool
Test if record
is a comment record.
GFF3.isdirective
— Methodisdirective(record::Record)::Bool
Test if record
is a directive record.
GFF3.isfeature
— Methodisfeature(record::Record)::Bool
Test if record
is a feature record.
GFF3.phase
— Methodphase(record::Record)::Int
Get the phase of record
.
GFF3.score
— Methodscore(record::Record)::Float64
Get the score of record
.
GFF3.seqend
— Methodseqend(record::Record)::Int
Get the end coordinate of record
.
GFF3.seqid
— Methodseqid(record::Record)::String
Get the sequence ID of record
.
GFF3.seqstart
— Methodseqstart(record::Record)::Int
Get the start coordinate of record
.
GFF3.source
— Methodsource(record::Record)::String
Get the source of record
.
GFF3.strand
— Methodstrand(record::Record)::GenomicFeatures.Strand
Get the strand of record
.