seqloc-0.5.1.1: Handle sequence locations for bioinformatics

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Bio.SeqLoc.Transcript

Contents

Synopsis

Type for splice junctions

newtype Junction Source

Splice junctions, which are isomorphic to the introns they span, but which support other biologically relevant constructors and accessors.

Constructors

Junction 

Fields

intron :: ContigLoc
 

fromDonorAcceptor :: Pos -> Pos -> JunctionSource

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).

donor :: Junction -> PosSource

Donor position, i.e., the last position in the 5' exon around a junction.

acceptor :: Junction -> PosSource

Acceptor position, i.e., the first position in the 3' exon around a junction.

junctions :: SpliceLoc -> [Junction]Source

List of splice junctions from a spliced location, in order.

Representation of transcript

data Transcript Source

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 

Fields

geneId :: !SeqLabel

Gene or locus name for a collection of transcripts

trxId :: !SeqLabel

Specific transcript identifier

location :: !SpliceSeqLoc

Sequence location of processed transcript

cds :: !(Maybe ContigLoc)

Location of CDS on the transcript

utr5 :: Transcript -> Maybe ContigLocSource

Just the location of the 5' UTR on the transcript, or Nothing if there is no cds on the transcript or if the cds location begins at the first nucleotide of the transcript--if a region is returned it will have positive length.

utr3 :: Transcript -> Maybe ContigLocSource

Just the location of the 3' UTR on the transcript, or Nothing if there is no cds on the transcript or if the cds location ends at the last nucleotide of the transcript--if a region is returned it will have positive length.

cdsLocation :: Transcript -> Maybe SpliceSeqLocSource

Genomic location of CDS within the transcript

sortContigs :: [ContigLoc] -> Maybe [ContigLoc]Source

Just the input contigs sorted in stranded order, when all lie on the same strand, or Nothing if they are not all on the same strand.