GTF_Record

Constructors

this

this(ubyte[] data)

constructor (raw ubytes)

this

this(string data)

constructor (string)

Members

Functions

attributes

string attributes(string field)

Column 9: attributes; A list of ;-separated feature attributes in key=value form

hasTag

bool hasTag()

Column 9 attributes may also include a comma-sep list of tags: (key:tag)={t1,t2,t3,...}

opIndex

string opIndex(string field)

Provides map key lookup semantics for column 9 attributes

toString

string toString()

Undocumented in source. Be warned that the author may not have intended to support it.

Properties

canonicalRepresentation

string canonicalRepresentation [@property getter]

Returns a string with the canonical "chr:start-end" representation

contig

contig [@property getter]

Column 1: seqid (aka contig); basis for the coordinate system

coordinateAtBegin

coordinateAtBegin [@property getter]

Genomic coordinate at beginning of feature, taking strandedness into account

coordinateAtEnd

coordinateAtEnd [@property getter]

Genomic coordinate at end of feature, taking strandedness into account

coordinateAtOffset

long coordinateAtOffset [@property setter]

Genomic coordinate at offset into feature, taking strandedness into account

coordinates

coordinates [@property getter]

Columns 4 & 5: returns Coordinate set: Obc format

end

end [@property getter]

Column 5: end; closed coordinate integer ending nucleotide position of the feature

isValid

bool isValid [@property getter]

TODO: Not implemented; (almost) always true

length

length [@property getter]

Computed feature length

phase

phase [@property getter]

Column 8: phase; For features of type "CDS", the phase indicates where the feature begins with reference to the reading frame. The phase is one of the integers 0, 1, or 2, indicating the number of bases that should be removed from the beginning of this feature to reach the first base of the next codon. In other words, a phase of "0" indicates that the next codon begins at the first base of the region described by the current line, a phase of "1" indicates that the next codon begins at the second base of this region, and a phase of "2" indicates that the codon begins at the third base of this region. This is NOT to be confused with the frame, which is simply start modulo 3.

relativeEnd

relativeEnd [@property getter]

Relative start === the feature length

relativeStart

relativeStart [@property getter]

Relative start === 1

score

score [@property getter]

Column 6: score; float. From the standard: "the semantics of the score are ill-defined." Tragically, score can be either a float, or not present (".") Totally arbitrarily, we will represent absent as -1

seqURI

string seqURI [@property getter]

Return the seqURI representation

seqid

seqid [@property getter]

Column 1: seqid (aka contig); basis for the coordinate system

source

source [@property getter]

Column 2: source; software, procedure, or database originating the record

start

start [@property getter]

Columns 4: start; 1-based integer start position of the feature

strand

strand [@property getter]

Column 7: strand; '+', '-', or '.' (or '?' for relevant but unknown)

type

type [@property getter]

Column 3: feature type; sequence ontology (SO) defined type, or SO accession number

• GTF_Record