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)]
• transType :: TranscriptType

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

data TranscriptType

Constructors

Coding

NonCoding

Instances

Eq TranscriptType

Defined in Bio.RealWorld.GENCODE

Methods

(==) :: TranscriptType -> TranscriptType -> Bool

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

Ord TranscriptType

Defined in Bio.RealWorld.GENCODE

Methods

compare :: TranscriptType -> TranscriptType -> Ordering

(<) :: TranscriptType -> TranscriptType -> Bool

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

(>) :: TranscriptType -> TranscriptType -> Bool

(>=) :: TranscriptType -> TranscriptType -> Bool

max :: TranscriptType -> TranscriptType -> TranscriptType

min :: TranscriptType -> TranscriptType -> TranscriptType

Show TranscriptType

Defined in Bio.RealWorld.GENCODE

Methods

showsPrec :: Int -> TranscriptType -> ShowS

show :: TranscriptType -> String

showList :: [TranscriptType] -> ShowS

readGenes :: FilePath -> IO [Gene]

Read gene information from Gencode GTF file

readGenesC :: Monad m => ConduitT ByteString o m [Gene]

getPromoters

Arguments

:: Int

upstream

-> Int

downstream

-> Gene

-> [BEDExt BED3 (Int, CI ByteString)]

getDomains

Arguments

:: BEDLike b

=> Int

Extension length. A good default is 1M.

-> [b]

A list of promoters

-> [b]

Regulatory domains

Compute genes' regulatory domains using the algorithm described in GREAT. NOTE: the result doesn't contain promoters