You can see an example in biofasta:
https://github.com/BioHaskell/biofasta/blob/master/src/Bio/Sequence/Fasta.hs
on line 31:
import Bio.Core.Sequence
then lines 37-44:
data Sequence = Seq SeqLabel SeqData (Maybe QualData)
deriving (Show, Eq)
instance BioSeq Sequence where
seqid (Seq lab seq mqual) = SeqLabel {unSL = B.takeWhile (/= '
') $ unSL lab}
seqheader (Seq lab seq mqual) = lab
seqdata (Seq lab seq mqual) = seq
seqlength (Seq lab seq mqual) = Offset {unOff = B.length $ unSD seq}
The BioSeq typeclass that is used above comes from Bio.Core.Sequence:
http://malde.org/~ketil/biohaskell/biocore/src/Bio/Core/Sequence.hs
-- | The 'BioSeq' class models sequence data, and any data object that
-- represents a biological sequence should implement it.
class BioSeq s where
seqid :: s -> SeqLabel -- ^ Sequence identifier (typically first
word of the header)
seqid = seqlabel
seqheader :: s -> SeqLabel -- ^ Sequence header (may contain
whitespace), by convention the
-- first word matches the 'seqid'
seqheader = seqlabel
seqdata :: s -> SeqData -- ^ Sequence data
seqlength :: s -> Offset -- ^ Sequence length
On Sat, Mar 29, 2014 at 3:07 AM, Vasili I. Galchin <vigalc...@gmail.com>wrote:
> Ketil,
>
> Maybe you misunderstood my question. Where is the new biocore used??
> Example please.
>
> Vasili
>
>
> On Sat, Mar 29, 2014 at 4:31 AM, Ketil Malde <ke...@malde.org> wrote:
>
>>
>> Vasili I. Galchin <vigalc...@gmail.com> writes:
>>
>> > I was under the impression that biocore replaces former
>> functionality
>> > like Bio.Sequence; however, just by random reading in
>> > http://hackage.haskell.org/package/bio-0.5.3/src/ .. I don't an import
>> of
>> > Bio.Core. Why?? I am trying to get TwoBit.hs in compliance with module
>> > Bio.Core.
>>
>> The idea is that biocore contains common definitions, but little
>> specific implementation. Which comes as separate libraries, so biofasta,
>> biofastq, etc are implementations for those formats.
>>
>> This way, TwoBit could have its own internal representation (possibly a
>> two-bit array), accessible through the "core" typeclasses.
>>
>> I started to work on making biolib (which is a monolithic library
>> containing all kinds of functionality) depend on biocore, but stumbled
>> upon some difficulties, and forgot about it.
>>
>> -k
>> --
>> If I haven't seen further, it is by standing in the footprints of giants
>>
>
>
