Since the default is the default, I'd like to see translateWith :: TransTable -> ...
translate = translateWith default_table by analogy with sort/sortBy. On Fri, Aug 26, 2011 at 05:53, Matt Fenwick <mfenwick...@gmail.com> wrote: > 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 > > _______________________________________________ Biohaskell mailing list Biohaskell@biohaskell.org http://malde.org/cgi-bin/mailman/listinfo/biohaskell
