Hi Dan, a common way to capture this pattern in Haskell is to use partially applied functions (I think this is also what Christian recommended).
The type for your function is: translate :: SeqData -> Offset -> Maybe TransTable -> SeqData But if you change the argument order to: translate :: TransTable -> SeqData -> Offset -> SeqData then you can add another function -- which is simply a partial application of translate (assuming defaulttable has been defined): defaultTranslate :: SeqData -> Offset -> SeqData defaultTranslate = translate defaulttable Caveats: 1. you have to change the order of arguments -- this may break existing code 2. the caller has two different function names to choose from -- is this a problem? I'm not sure Advantages: 1. one implementation 2. no 'Maybe's to make things complicated 3. other 'default' tables could be swapped in, through the use of additional partial applications of 'translate' On Fri, Aug 26, 2011 at 6:00 AM, <biohaskell-requ...@biohaskell.org> wrote: > Send Biohaskell mailing list submissions to > biohaskell@biohaskell.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://malde.org/cgi-bin/mailman/listinfo/biohaskell > or, via email, send a message with subject or body 'help' to > biohaskell-requ...@biohaskell.org > > You can reach the person managing the list at > biohaskell-ow...@biohaskell.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Biohaskell digest..." > > > Today's Topics: > > 1. Re: Mitochondrial Translation Table (Dan Fornika) > 2. Re: Mitochondrial Translation Table (Ketil Malde) > 3. Re: Mitochondrial Translation Table > (Christian H?ner zu Siederdissen) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 25 Aug 2011 18:53:40 -0700 > From: Dan Fornika <dforn...@gmail.com> > To: biohaskell@biohaskell.org > Subject: Re: [Biohaskell] Mitochondrial Translation Table > Message-ID: <4e56fca4.4090...@gmail.com> > Content-Type: text/plain; charset="iso-8859-1"; Format="flowed" > > 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 > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: Translation.hs > Type: text/x-haskell > Size: 6809 bytes > Desc: not available > URL: < > http://malde.org/pipermail/biohaskell/attachments/20110825/b5bc6166/attachment-0001.hs > > > > ------------------------------ > > Message: 2 > Date: Fri, 26 Aug 2011 06:06:49 +0200 > From: Ketil Malde <ke...@malde.org> > To: biohaskell@biohaskell.org > Subject: Re: [Biohaskell] Mitochondrial Translation Table > Message-ID: <874o143jfq....@malde.org> > Content-Type: text/plain; charset=us-ascii > > Dan Fornika <dforn...@gmail.com> writes: > > > 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. > > Okay. > > > Does it make sense to write this with the type signature: > > > translate :: SeqData -> Offset -> Maybe TransTable -> SeqData > > To some extent. You'll need to supply 'Nothing' as the third parameter, > so you might as well write 'default_table' or some such, avoiding the > maybe. > > > 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. > > Variable number of arguments is possible (see e.g. Printf) but it > involves some trickery. I think it might not be worth it, and suggest > 'translate' always take an argument, possibly with a specialized > 'translateStd' function supplying the default argument. > > Regarding the implementation, you can simplify the 'translate' function > (since it basically repeats the same function twice) by using something > like: > > translate s' o' mb_tab = unfoldr codons (s',o',mytable) > where mytable = fromMaybe trans_table_std mb_tab > codons (s, o, trans_table) = .... > > Also, -Wall will warn you about recycling names, which can cause errors. > > -k > -- > If I haven't seen further, it is by standing in the footprints of giants > > > ------------------------------ > > Message: 3 > Date: Fri, 26 Aug 2011 11:22:29 +0200 > From: Christian H?ner zu Siederdissen <choe...@tbi.univie.ac.at> > To: Dan Fornika <dforn...@gmail.com> > Cc: biohaskell@biohaskell.org > Subject: Re: [Biohaskell] Mitochondrial Translation Table > Message-ID: <20110826092229.GA2001@workstation> > Content-Type: text/plain; charset="us-ascii" > > 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 > > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: not available > Type: application/pgp-signature > Size: 198 bytes > Desc: not available > URL: < > http://malde.org/pipermail/biohaskell/attachments/20110826/a145e643/attachment-0001.pgp > > > > ------------------------------ > > _______________________________________________ > Biohaskell mailing list > Biohaskell@biohaskell.org > http://malde.org/cgi-bin/mailman/listinfo/biohaskell > > > End of Biohaskell Digest, Vol 9, Issue 4 > **************************************** >
_______________________________________________ Biohaskell mailing list Biohaskell@biohaskell.org http://malde.org/cgi-bin/mailman/listinfo/biohaskell
