GFFRecord

GFF Generic Record

Format Documentation: http://gmod.org/wiki/GFF2#The_GFF2_File_Format

https://useast.ensembl.org/info/website/upload/gff.html

Represents a GFF record. Version selected only changes formatting of String representations and how the record is parsed. Implementation is mostly the same. This record has getters and setters and should be able to be built from scratch.

struct GFFRecord (

GFFVersion ver

) {

this(ubyte[] data);

this(string data);

bool isValid [@property getter];

seqid [@property getter];

string seqid [@property setter];

contig [@property getter];

string contig [@property setter];

source [@property getter];

string source [@property setter];

type [@property getter];

string type [@property setter];

coordinates [@property getter];

Interval!cs coordinates [@property setter];

start [@property getter];

end [@property getter];

score [@property getter];

float score [@property setter];

strand [@property getter];

char strand [@property setter];

phase [@property getter];

long phase [@property setter];

group [@property getter];

string group [@property setter];

string attributes(string field);

string opIndex(string field);

void opIndexAssign(string val, string field);

bool hasTag();

length [@property getter];

relativeStart [@property getter];

relativeEnd [@property getter];

long coordinateAtOffset [@property setter];

coordinateAtBegin [@property getter];

coordinateAtEnd [@property getter];

string toString();

string canonicalRepresentation [@property getter];

string seqURI [@property getter];

}

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
opIndexAssign void opIndexAssign(string val, string field): Provides map key assignment 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]
string contig [@property setter]: Column 1: seqid (aka contig); basis for the coordinate system setter
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 getter
coordinates Interval!cs coordinates [@property setter]: Columns 4 & 5: returns Coordinate set: OBC format setter
end end [@property getter]: Column 5: end; closed coordinate integer ending nucleotide position of the feature
group group [@property getter]: Column 9: backwards compatible GFF2 group field
group string group [@property setter]: Column 9: backwards compatible GFF2 group field
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.
phase long phase [@property setter]: Undocumented in source. Be warned that the author may not have intended to support it.
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 getter
score float score [@property setter]: 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 setter
seqURI string seqURI [@property getter]: Return the seqURI representation
seqid seqid [@property getter]: Column 1: seqid (aka contig); basis for the coordinate system getter
seqid string seqid [@property setter]: Column 1: seqid (aka contig); basis for the coordinate system setter
source source [@property getter]: Column 2: source; software, procedure, or database originating the record getter
source string source [@property setter]: Column 2: source; software, procedure, or database originating the record setter
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)
strand char strand [@property setter]: 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 getter
type string type [@property setter]: Column 3: feature type; sequence ontology (SO) defined type, or SO accession number setter

GFFRecord

Constructors

Members

Functions

Properties

Meta

Source