Bio.RealWorld.UCSC

Documentation

data UCSCGene

Constructors

UCSCGene

Fields

• _geneName :: !ByteString
• _chrom :: !ByteString
• _strand :: !Bool
• _transcript :: !(Int, Int)
• _cds :: !(Int, Int)
• _exons :: !(Vector (Int, Int))
• _introns :: !(Vector (Int, Int))
• _proteinId :: !UniprotID
• _alignId :: !UCSCID

Instances

Show UCSCGene

Methods

showsPrec :: Int -> UCSCGene -> ShowS

show :: UCSCGene -> String

showList :: [UCSCGene] -> ShowS

getTSS :: UCSCGene -> (ByteString, Int)

get Transcription Start Site

getJunction :: UCSCGene -> (ByteString, Vector Int)

get exon-intron junctions

readUCSCGenes :: FilePath -> Source IO UCSCGene

read genes from UCSC "knownGenes.tsv"

readUCSCGenes' :: FilePath -> IO [UCSCGene]