bio-0.4.5: A bioinformatics librarySource codeContentsIndex

Functionality for manipulating KEGG annotations.

KEGG is a bit hard find, but there exist species-specific tables Available organisms are listed in the table at

Data for each organism is stored its own subdirectory under

Containing tables linking everything -- including external resources like UniProt, PDB, or NCBI -- together.

genReadKegg :: FilePath -> IO [(ByteString, ByteString)]
newtype KO = KO ByteString
decodeUP :: ByteString -> UniProtAcc
decodeKO :: ByteString -> KO
removePrefix :: String -> String -> (ByteString -> a) -> ByteString -> a
genReadKegg :: FilePath -> IO [(ByteString, ByteString)]Source
Most KEGG files that contain associations, have one association per line, consisting of two items separated by whitespace. This is a generalized reader function.
newtype KO Source
KO ByteString
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decodeUP :: ByteString -> UniProtAccSource
Convert UniProt IDs (up:xxxxxx) to the UniProtAcc type.
decodeKO :: ByteString -> KOSource
Convert KO IDs (ko:xxxxx) to the KO data type.
removePrefix :: String -> String -> (ByteString -> a) -> ByteString -> aSource
KEGG uses strings with an identifying prefix for IDs. This helper function checks and removes prefix to construct native values.
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