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SHORE API
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SHORE API
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GFF3 annotation entry. More...
Public Types | |
| enum | Phase { PHASE_NA =-1, PHASE_0 =0, PHASE_1 =1, PHASE_2 =2 } |
Static Public Member Functions | |
| static bool | is_score_NA (const double &score) |
Public Attributes | |
| std::string | seqid |
| std::string | source |
| std::string | type |
| long | pos |
| long | end |
| double | score |
| shore::ExtendedStrand | strand |
| Phase | phase |
| std::vector< std::string > | other_attributes |
| All attributes other than the ones described below. More... | |
| std::string | id |
| Indicates the ID of the feature. More... | |
| std::string | name |
| std::string | alias |
| std::string | parent |
| std::string | target |
| std::string | gap |
| std::string | derives_from |
| std::string | note |
| Note A free text note. | |
| std::string | dbxref |
| std::string | ontology_term |
| bool | is_circular |
| A flag to indicate whether a feature is circular. | |
GFF3 annotation entry.
Variable descriptions from http://www.sequenceontology.org/resources/gff3.html.
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 field. The phase is REQUIRED for all CDS features.
| std::string shore::annotation_entry::alias |
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.
| std::string shore::annotation_entry::dbxref |
Dbxref A database cross reference. See the section "Ontology Associations and Db Cross References" for details on the format.
| std::string shore::annotation_entry::derives_from |
Derives_from 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.
| std::string shore::annotation_entry::gap |
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 Exonerate documentation. See "THE GAP ATTRIBUTE" for a description of this format.
| std::string shore::annotation_entry::id |
Indicates the ID of the feature.
IDs for each feature must be unique within the scope of the GFF file. In the case of discontinuous features (i.e. a single feature that exists over multiple genomic locations) the same ID may appear on multiple lines. All lines that share an ID collectively represent a single feature.
| std::string shore::annotation_entry::name |
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.
| std::string shore::annotation_entry::ontology_term |
Ontology_term A cross reference to an ontology term. See the section "Ontology Associations and Db Cross References" for details.
| std::vector<std::string> shore::annotation_entry::other_attributes |
All attributes other than the ones described below.
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.
| std::string shore::annotation_entry::parent |
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 relationship.
| long shore::annotation_entry::pos |
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 features that cross the origin of a circular feature (e.g. most bacterial genomes, plasmids, and some viral genomes), the requirement for start to be less than or equal to end is satisfied by making end = the position of the end + the length of the landmark feature. 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.
| double shore::annotation_entry::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 prediction features.
| std::string shore::annotation_entry::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.:^*$@!+_?-|]. In particular, IDs may not contain unescaped whitespace and must not begin with an unescaped ">".
| std::string shore::annotation_entry::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.
| shore::ExtendedStrand shore::annotation_entry::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.
| std::string shore::annotation_entry::target |
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.
| std::string shore::annotation_entry::type |
The type of the feature (previously called the "method"). This is constrained to be either: (a)a term from the "lite" version of the Sequence Ontology - SOFA, a term from the full Sequence Ontology - it must be an is_a child of sequence_feature (SO:0000110) or (c) a SOFA or SO accession number. The latter alternative is distinguished using the syntax SO:000000.
1.8.4 
