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Bio.Sequence.KEGG
Description
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 ftp://ftp.genome.jp/pub/kegg/genes/etc/all_species.tab Data for each organism is stored its own subdirectory under ftp://ftp.genome.jp/pub/kegg/genes/organisms/ Containing tables linking everything -- including external resources like UniProt, PDB, or NCBI -- together.
Synopsis
genReadKegg :: FilePath -> IO [(ByteString, ByteString)]
newtype KO = KO ByteString
decodeUP :: ByteString -> UniProtAcc
decodeKO :: ByteString -> KO
removePrefix :: String -> String -> (ByteString -> a) -> ByteString -> a
Documentation
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
Constructors
KO ByteString |
Instances
Show KO
decodeUP :: ByteString -> UniProtAcc | Source
Convert UniProt IDs (up:xxxxxx) to the UniProtAcc type.
decodeKO :: ByteString -> KO | Source
Convert KO IDs (ko:xxxxx) to the KO data type.
removePrefix :: String -> String -> (ByteString -> a) -> ByteString -> a | Source
KEGG uses strings with an identifying prefix for IDs. This helper function checks and removes prefix to construct native values.
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