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 :: ![Transcript]

Instances

Eq Gene

Defined in Bio.RealWorld.GENCODE

Methods

(==) :: Gene -> Gene -> Bool

(/=) :: Gene -> Gene -> Bool

Ord Gene

Defined in Bio.RealWorld.GENCODE

Methods

compare :: Gene -> Gene -> Ordering

(<) :: Gene -> Gene -> Bool

(<=) :: Gene -> Gene -> Bool

(>) :: Gene -> Gene -> Bool

(>=) :: Gene -> Gene -> Bool

max :: Gene -> Gene -> Gene

min :: Gene -> Gene -> Gene

Show Gene

Defined in Bio.RealWorld.GENCODE

Methods

showsPrec :: Int -> Gene -> ShowS

show :: Gene -> String

showList :: [Gene] -> ShowS

data Transcript

Constructors

Transcript

Fields

• transId :: !ByteString
• transLeft :: !Int
• transRight :: !Int
• transStrand :: !Bool
• transExon :: ![(Int, Int)]
• transUTR :: ![(Int, Int)]

Instances

Eq Transcript

Defined in Bio.RealWorld.GENCODE

Methods

(==) :: Transcript -> Transcript -> Bool

(/=) :: Transcript -> Transcript -> Bool

Ord Transcript

Defined in Bio.RealWorld.GENCODE

Methods

compare :: Transcript -> Transcript -> Ordering

(<) :: Transcript -> Transcript -> Bool

(<=) :: Transcript -> Transcript -> Bool

(>) :: Transcript -> Transcript -> Bool

(>=) :: Transcript -> Transcript -> Bool

max :: Transcript -> Transcript -> Transcript

min :: Transcript -> Transcript -> Transcript

Show Transcript

Defined in Bio.RealWorld.GENCODE

Methods

showsPrec :: Int -> Transcript -> ShowS

show :: Transcript -> String

showList :: [Transcript] -> ShowS

readGenes :: FilePath -> IO [Gene]

Read gene information from Gencode GTF file