Safe Haskell | None |
---|---|
Language | Haskell2010 |
Bio.SeqLoc.Transcript
- newtype Junction = Junction {}
- fromDonorAcceptor :: Pos -> Pos -> Junction
- donor :: Junction -> Pos
- acceptor :: Junction -> Pos
- junctions :: SpliceLoc -> [Junction]
- data Transcript = Transcript {}
- utr5 :: Transcript -> Maybe ContigLoc
- utr3 :: Transcript -> Maybe ContigLoc
- cdsLocation :: Transcript -> Maybe SpliceSeqLoc
- sortContigs :: [ContigLoc] -> Maybe [ContigLoc]
Type for splice junctions
Splice junctions, which are isomorphic to the introns they span, but which support other biologically relevant constructors and accessors.
fromDonorAcceptor :: Pos -> Pos -> Junction #
Create a splice junction from a donor position (the last position in the 5' exon) and the acceptor position (the first position in the 3' exon).
Acceptor position, i.e., the first position in the 3' exon around a junction.
Representation of transcript
data Transcript #
Representation of a genomic transcript, with a gene and a transcript identifier, along with the genomic location of the processed transcript and an optional coding sequence on that transcript.
Constructors
Transcript | |
Instances
utr5 :: Transcript -> Maybe ContigLoc #
utr3 :: Transcript -> Maybe ContigLoc #
cdsLocation :: Transcript -> Maybe SpliceSeqLoc #
Genomic location of CDS within the transcript