I'm having trouble testing my code out in ghci. I've been loading the Bio.Core module, abut I get error messages saying that:
Not in scope: data constructor `SeqData'Shouldn't that data constructor be in scope because Bio.Core exports Bio.Core.Sequence, which in turn contains the expression:
type SeqData = LC.ByteString ? Dan On 26/08/11 10:04 AM, Aaron D. Ball wrote:
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 -> SeqDataTo 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. -kimport 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... 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