Bio.RealWorld.GENCODE

Documentation

data Gene

GTF's position is 1-based, but here we convert it to 0-based indexing.

Constructors

Gene

Fields

• geneName :: !(CI ByteString)
• geneId :: !ByteString
• geneChrom :: !ByteString
• geneLeft :: !Int
• geneRight :: !Int
• geneStrand :: !Bool
• geneTranscripts :: ![(Int, Int)]
• geneExon :: ![(Int, Int)]

Instances

Show Gene

Defined in Bio.RealWorld.GENCODE

Methods

showsPrec :: Int -> Gene -> ShowS

show :: Gene -> String

showList :: [Gene] -> ShowS

readGenes :: FilePath -> IO [Gene]

Read gene information from Gencode GTF file

streamElements :: Monad m => ConduitT ByteString BED m ()