public class GFF3Reader
- extends Object
GFF3 Format has
Undefined fields are replaced with the "." character, as described in
the original GFF spec.
Column 1: "seqid"
The ID of the landmark used to establish the coordinate system for the
current feature. IDs may contain any characters, but must escape any
characters not in the set [a-zA-Z0-9.:ˆ*$@!+_?-|]. In particular, IDs
may not contain unescaped whitespace and must not begin with an
Column 2: "source"
The source is a free text qualifier intended to describe the algorithm
or operating procedure that generated this feature. Typically this is
the name of a piece of software, such as "Genescan" or a database
name, such as "Genbank." In effect, the source is used to extend the
feature ontology by adding a qualifier to the type creating a new
composite type that is a subclass of the type in the type column.
Column 3: "type"
The type of the feature (previously called the "method"). This is
constrained to be either: (a) a term from the "lite" sequence
ontology, SOFA; or (b) a SOFA accession number. The latter
alternative is distinguished using the syntax SO:000000.
Columns 4 & 5: "start" and "end"
The start and end of the feature, in 1-based integer coordinates,
relative to the landmark given in column 1. Start is always less than
or equal to end.
For zero-length features, such as insertion sites, start equals end
and the implied site is to the right of the indicated base in the
direction of the landmark.
Column 6: "score"
The score of the feature, a floating point number. As in earlier
versions of the format, the semantics of the score are ill-defined.
It is strongly recommended that E-values be used for sequence
similarity features, and that P-values be used for ab initio gene
Column 7: "strand"
The strand of the feature. + for positive strand (relative to the
landmark), - for minus strand, and . for features that are not
stranded. In addition, ? can be used for features whose strandedness
is relevant, but unknown.
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.
For forward strand features, phase is counted from the start
field. For reverse strand features, phase is counted from the end
The phase is REQUIRED for all CDS features.
Column 9: "attributes"
A list of feature attributes in the format tag=value. Multiple
tag=value pairs are separated by semicolons. URL escaping rules are
used for tags or values containing the following characters: ",=;".
Spaces are allowed in this field, but tabs must be replaced with the
%09 URL escape.
These tags have predefined meanings:
ID Indicates the name of the feature. IDs must be unique
within the scope of the GFF file.
Name Display name for the feature. This is the name to be
displayed to the user. Unlike IDs, there is no requirement
that the Name be unique within the file.
Alias A secondary name for the feature. It is suggested that
this tag be used whenever a secondary identifier for the
feature is needed, such as locus names and
accession numbers. Unlike ID, there is no requirement
that Alias be unique within the file.
Parent Indicates the parent of the feature. A parent ID can be
used to group exons into transcripts, transcripts into
genes, an so forth. A feature may have multiple parents.
Parent can *only* be used to indicate a partof
Target Indicates the target of a nucleotide-to-nucleotide or
protein-to-nucleotide alignment. The format of the
value is "target_id start end [strand]", where strand
is optional and may be "+" or "-". If the target_id
contains spaces, they must be escaped as hex escape %20.
Gap The alignment of the feature to the target if the two are
not collinear (e.g. contain gaps). The alignment format is
taken from the CIGAR format described in the
?cvsroot=Ensembl). See "THE GAP ATTRIBUTE" for a description
of this format.
Used to disambiguate the relationship between one
feature and another when the relationship is a temporal
one rather than a purely structural "part of" one. This
is needed for polycistronic genes. See "PATHOLOGICAL CASES"
for further discussion.
Note A free text note.
Dbxref A database cross reference. See the section
"Ontology Associations and Db Cross References" for
details on the format.
Ontology_term A cross reference to an ontology term. See
the section "Ontology Associations and Db Cross References"
Multiple attributes of the same type are indicated by separating the
values with the comma "," character, as in:
Note that attribute names are case sensitive. "Parent" is not the
same as "parent".
All attributes that begin with an uppercase letter are reserved for
later use. Attributes that begin with a lowercase letter can be used
freely by applications.
|Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
public GFF3Reader(Reader input)
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