Bio.Seq.IO

Documentation

data Genome

The first 2048 bytes are header. Header consists of a magic string, followed by chromosome information. Example: HASKELLBIOINFORMATICSnCHR1 START SIZE

openGenome :: FilePath -> IO Genome

closeGenome :: Genome -> IO ()

withGenome :: FilePath -> (Genome -> IO a) -> IO a

getSeq :: BioSeq s a => Genome -> Query -> IO (Either String (s a))

Retrieve sequence.

getChrom :: Genome -> ByteString -> IO (Either String (DNA IUPAC))

Retrieve whole chromosome.

getChrSizes :: Genome -> [(ByteString, Int)]

Retrieve chromosome size information.

mkIndex

Arguments

:: [FilePath]

A list of fasta files. Each file can have multiple chromosomes.

-> FilePath

output file

-> IO ()

Indexing a genome.