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Bio.Sequence.TwoBit

Description
This module implements the 2bit format for sequences. Based on: http://genome.ucsc.edu/FAQ/FAQformat#format7 Note! the description is not accurate, it is missing a reserved word in each sequence record. There are also other, completely different ideas of the 2bit format, e.g. http://jcomeau.freeshell.org/www/genome/2bitformat.html
Synopsis

decode2Bit :: ByteString -> [Sequence Unknown]
read2Bit :: FilePath -> IO [Sequence Unknown]
hRead2Bit :: Handle -> IO [Sequence Unknown]
encode2Bit :: [Sequence a] -> ByteString
write2Bit :: FilePath -> [Sequence a] -> IO ()
hWrite2Bit :: Handle -> [Sequence a] -> IO ()

Documentation

decode2Bit :: ByteString -> [Sequence Unknown] | Source

Parse a (lazy) ByteString as sequences in the 2bit format.

read2Bit :: FilePath -> IO [Sequence Unknown] | Source

Read sequences from a file in 2bit format and | unmarshall/deserialize into Sequence format.

hRead2Bit :: Handle -> IO [Sequence Unknown] | Source

Read sequences from a file handle in the 2bit format and | unmarshall/deserialze into Sequence format.

encode2Bit :: [Sequence a] -> ByteString | Source

Marshall from neutral representation to the 2Bit ByteString rep

write2Bit :: FilePath -> [Sequence a] -> IO () | Source

Marshall/serialize [Sequence] into 2Bit format and write to a file.

hWrite2Bit :: Handle -> [Sequence a] -> IO () | Source

Marshall/serialize [Sequence] into 2Bit format and write to a file using handle.
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