Hi, there are a number of possibilities:
(i) implicit parameters ;-) http://www.haskell.org/ghc/docs/7.0.3/html/users_guide/other-type-extensions.html#implicit-parameters (ii) this thing http://neilmitchell.blogspot.com/2008/04/optional-parameters-in-haskell.html (iii) what I prefer myfun :: a -> b -> c myFun a b = "complicated stuff" defFun = myFun (default a) Gruss, Christian * Dan Fornika <dforn...@gmail.com> [26.08.2011 03:56]: > Hello, > > I've gotten a start on this but am running into a few difficulties. > I've attached my code so far. > > I'd like to implement a function "translate" that uses the standard > translation table by default, but can optionally use a different > translation table if it is passed as an argument. Does it make > sense to write this with the type signature: > > translate :: SeqData -> Offset -> Maybe TransTable -> SeqData > > I'd like to be able to call the function with only the first two > argument and get the hard-coded standard translation table, but if I > pass a third argument with type TransTable, I get the customized > translation. > > As I've mentioned before on this list I'm still quite new to > haskell, so any tips are appreciated. > > Dan > > On 16/08/11 02:16 PM, Ketil Malde wrote: > >Dan Fornika<dforn...@gmail.com> writes: > > > >>I've been working on a mitochondrial genetics project, and I'd like to > >>see a human mitochondrial-specific translation function integrated > >>into BioHaskell. > > > >Hm, yes, support for the non-canonical translations would be nice. > > > >>I see that Bio.Sequence.Phd has a standard translation table, > > > >Bio.Sequence.SeqData, actually, but it's reexported in a lot of places. > > > >>so I've > >>made a version called trans_tbl_mito with the appropriate changes > >>integrated. > > > >Currently, there's just a 'translate' that hardwires this table. I > >concede this is poor design, the table ought to be a parameter, but it > >was what I needed at the time. > > > >>I know that there is a lot of re-factoring going on, and > >>I'm not sure what is the most efficient/elegant way to introduce this > >>feature. > > > >How about a module Bio.Sequence.Translation containing: > > > > import Bio.Core.Sequence > > > > data Triple = ... -- e.g. String, or perhaps just SeqData > > data Amino = ... > > data TransTable = [(Triple,Amino)] > > > > transtable_std, transtbl_mito, ... :: TransTable > > > > translate :: TransTable -> SeqData -> SeqData > > > > -- and perhaps versions for all frames, or some specific frame? > > > >What does everybody think? > > > >Dan: would you like to write this? Feel free to rip what you want from > >the old SeqData module. > > > >-k > import Bio.Core.Sequence > > import Data.List (unfoldr, intercalate, isPrefixOf) > import Data.Char (toUpper, isNumber) > import Data.Maybe > import qualified Data.ByteString.Lazy.Char8 as B > import qualified Data.ByteString.Lazy as BB > > data Codon = String -- SeqData? > > data Amino = Ala | Arg | Asn | Asp | Cys | Gln | Glu | Gly > | His | Ile | Leu | Lys | Met | Phe | Pro | Ser > | Thr | Tyr | Trp | Val > | STP | Asx | Glx | Xle | Xaa -- unknowns > deriving (Show,Eq) > > data TransTable = TTable [(Codon, Amino)] > > data InverseTransTable = ITTable [(Amino, Codon)] > > {-# INLINE (!) #-} > (!) :: SeqData -> Offset -> Char > (!) (SeqData bs) = B.index bs > > translate :: SeqData -> Offset -> Maybe TransTable -> SeqData > translate s' o' Nothing = unfoldr codons (s', o') > where codons (s,o) = > if o > seqlength s - 3 then Nothing > else Just (trans1 (map (s!) [o, o+1, o+2]), (s, o+3) > trans_table_std) > translate s' o' trans_table = unfoldr codons (s', o', trans_table) > where codons (s, o, trans_table) = > if o > seqlength s - 3 then Nothing > else Just (trans1 (map (s!) [o, o+1, o+2]), (s, o+3) trans_table) > > trans1 :: String -> Maybe TransTable-> Amino > trans1 s Nothing = (flip lookup trans_table_std . map (repUT . toUpper)) s > where repUT x = if x == 'U' then 'T' else x -- RNA uses U for T > trans1 s transl_table = (flip lookup transl_table . map (repUT . toUpper)) s > where repUT x = if x == 'U' then 'T' else x -- RNA uses U for T > > -- amino2iupac :: [Amino] -> SeqData > -- amino2iupac = > > -- reverse_translate :: SeqData -> TransTable -> SeqData > -- reverse_translate = > > -- rev_trans1 :: Amino -> TransTable -> String > -- rev_trans1 = > > -- todo: extend with more IUPAC nucleotide wildcards? > -- | Convert a list of amino acids to a sequence in IUPAC format. > toIUPAC :: [Amino] -> SeqData > toIUPAC = B.pack . map (fromJust . flip lookup iupac) > > -- | Convert a sequence in IUPAC format to a list of amino acids. > fromIUPAC :: SeqData -> [Amino] > fromIUPAC = map (maybe Xaa id . flip lookup iupac' . toUpper) . B.unpack > > iupac :: [(Amino, Char)] > iupac = [(Ala, 'A'), (Arg, 'R'), (Asn, 'N') > ,(Asp, 'D'), (Cys, 'C'), (Gln, 'Q') > ,(Glu, 'E'), (Gly, 'G'), (His, 'H') > ,(Ile, 'I'), (Leu, 'L'), (Lys, 'K') > ,(Met, 'M'), (Phe, 'F'), (Pro, 'P') > ,(Ser, 'S'), (Thr, 'T'), (Tyr, 'Y') > ,(Trp, 'W'), (Val,'V') > ,(Asx, 'B') -- Asn or Asp > ,(Glx, 'Z') -- Gln or Glu > ,(Xle, 'J') -- Ile or Leu > ,(STP, '*') > ,(Xaa, 'X') > ] > > iupac' :: [(Char,Amino)] > iupac' = map (\(a,b)->(b,a)) iupac > > trans_table_std :: TransTable > trans_table_std = TTable [("AAA", Lys), ("AAC", Asn), ("AAG", Lys), ("AAT", > Asn) > ,("ACA", Thr), ("ACC", Thr), ("ACG", Thr), ("ACT", > Thr) > ,("AGA", Arg), ("AGC", Ser), ("AGG", Arg), ("AGT", > Ser) > ,("ATA", Ile), ("ATC", Ile), ("ATG", Met), ("ATT", > Ile) > ,("CAA", Gln), ("CAC", His), ("CAG", Gln), ("CAT", > His) > ,("CCA", Pro), ("CCC", Pro), ("CCG", Pro), ("CCT", > Pro) > ,("CGA", Arg), ("CGC", Arg), ("CGG", Arg), ("CGT", > Arg), > ,("CTA", Leu), ("CTC", Leu), ("CTG", Leu), ("CTT", > Leu), > ,("GAA", Glu), ("GAC", Asp), ("GAG", Glu), ("GAT", > Asp), > ,("GCA", Ala), ("GCC", Ala), ("GCG", Ala), ("GCT", > Ala), > ,("GGA", Gly), ("GGC", Gly), ("GGG", Gly), ("GGT", > Gly), > ,("GTA", Val), ("GTC", Val), ("GTG", Val), ("GTT", > Val), > ,("TAA", STP), ("TAC", Tyr), ("TAG", STP), ("TAT", > Tyr), > ,("TCA", Ser), ("TCC", Ser), ("TCG", Ser), ("TCT", > Ser), > ,("TGA", STP), ("TGC", Cys), ("TGG", Trp), ("TGT", > Cys), > ,("TTA", Leu), ("TTC", Phe), ("TTG", Leu), ("TTT", > Phe) > -- ("RAT", Asx), ("RAC", Asx), ("SAA", Glx), ("SAG", > Glx) > -- IUPAC R is (A or G), S is (C or G) > ] > > trans_table_vertebrate_mito :: TransTable > trans_table_vertebrate_mito = TTable [ > , ("AAA", Lys), ("AAC", Asn), ("AAG", > Lys), ("AAT", Asn), > ("ACA", Thr), ("ACC", Thr), ("ACG", Thr), ("ACT", Thr), > ("AGA", STP), ("AGC", Ser), ("AGG", STP), ("AGT", Ser), > ("ATA", Met), ("ATC", Ile), ("ATG", Met), ("ATT", Ile), > ("CAA", Gln), ("CAC", His), ("CAG", Gln), ("CAT", His), > ("CCA", Pro), ("CCC", Pro), ("CCG", Pro), ("CCT", Pro), > ("CGA", Arg), ("CGC", Arg), ("CGG", Arg), ("CGT", Arg), > ("CTA", Leu), ("CTC", Leu), ("CTG", Leu), ("CTT", Leu), > ("GAA", Glu), ("GAC", Asp), ("GAG", Glu), ("GAT", Asp), > ("GCA", Ala), ("GCC", Ala), ("GCG", Ala), ("GCT", Ala), > ("GGA", Gly), ("GGC", Gly), ("GGG", Gly), ("GGT", Gly), > ("GTA", Val), ("GTC", Val), ("GTG", Val), ("GTT", Val), > ("TAA", STP), ("TAC", Tyr), ("TAG", STP), ("TAT", Tyr), > ("TCA", Ser), ("TCC", Ser), ("TCG", Ser), ("TCT", Ser), > ("TGA", Trp), ("TGC", Cys), ("TGG", Trp), ("TGT", Cys), > ("TTA", Leu), ("TTC", Phe), ("TTG", Leu), ("TTT", Phe) > --("RAT", Asx), ("RAC", Asx), ("SAA", Glx), ("SAG", Glx) --IUPAC R is (A or > G), S is (C or G) > ] > > trans_table_yeast_nuc :: TransTable > trans_table_yeast_nuc = TTable [ > ("AAA", Lys), ("AAC", Asn), ("AAG", Lys), ("AAT", Asn), > ("ACA", Thr), ("ACC", Thr), ("ACG", Thr), ("ACT", Thr), > ("AGA", Arg), ("AGC", Ser), ("AGG", Arg), ("AGT", Ser), > ("ATA", Met), ("ATC", Ile), ("ATG", Met), ("ATT", Ile), > ("CAA", Gln), ("CAC", His), ("CAG", Gln), ("CAT", His), > ("CCA", Pro), ("CCC", Pro), ("CCG", Pro), ("CCT", Pro), > ("CGA", Arg), ("CGC", Arg), ("CGG", Arg), ("CGT", Arg), > ("CTA", Leu), ("CTC", Thr), ("CTG", Thr), ("CTT", Thr), > ("GAA", Glu), ("GAC", Asp), ("GAG", Glu), ("GAT", Asp), > ("GCA", Ala), ("GCC", Ala), ("GCG", Ala), ("GCT", Ala), > ("GGA", Gly), ("GGC", Gly), ("GGG", Gly), ("GGT", Gly), > ("GTA", Val), ("GTC", Val), ("GTG", Val), ("GTT", Val), > ("TAA", STP), ("TAC", Tyr), ("TAG", STP), ("TAT", Tyr), > ("TCA", Ser), ("TCC", Ser), ("TCG", Ser), ("TCT", Ser), > ("TGA", Trp), ("TGC", Cys), ("TGG", Trp), ("TGT", Cys), > ("TTA", Leu), ("TTC", Phe), ("TTG", Leu), ("TTT", Phe) > --("RAT", Asx), ("RAC", Asx), ("SAA", Glx), ("SAG", Glx) --IUPAC R is (A or > G), S is (C or G) > ] > > inverse_trans_table_std :: InverseTransTable > inverse_trans_table_std = ITTable [ > (Ala, "GCN"), (Leu, "YTN"), (Arg, "MGN"), (Lys, "AAR"), > (Asn, "AAY"), (Met, "ATG"), (Asp, "GAY"), (Phe, "TTY"), > (Cys, "TGY"), (Pro, "CCN"), (Gln, "CAR"), (Ser, "WSN"), > (Glu, "GAR"), (Thr, "ACN"), (Gly, "GGN"), (Trp, "TGG"), > (His, "CAY"), (Tyr, "TAY"), (Ile, "AUH"), (Val, "GUN"), > (STP, "TRR"), (Asx, "RAY"), (Glx, "SAR"), (Xaa, "NNN") > ] > _______________________________________________ > Biohaskell mailing list > Biohaskell@biohaskell.org > http://malde.org/cgi-bin/mailman/listinfo/biohaskell
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