Safe Haskell	None
Language	Haskell98

Bio.Core.Sequence

Contents

Data definitions
Class definitions
Helper functions

Description

This module defines common data structures for biosequences, i.e. data that represents nucleotide or protein sequences.

Basically, anything resembling or wrapping a sequence should implement the BioSeq class (and BioSeqQual if quality information is available).

The data types are mostly wrappers from lazy bytestrings from Lazy and Char8, but most users of this module should not need to access the underlying data types directly.

Synopsis

Data definitions

newtype Qual #

A quality value is in the range 0..255.

Constructors

Qual
Fields unQual :: Word8

Instances

Enum Qual #
Methods succ :: Qual -> Qual # pred :: Qual -> Qual # toEnum :: Int -> Qual # fromEnum :: Qual -> Int # enumFrom :: Qual -> [Qual] # enumFromThen :: Qual -> Qual -> [Qual] # enumFromTo :: Qual -> Qual -> [Qual] # enumFromThenTo :: Qual -> Qual -> Qual -> [Qual] #
Eq Qual #
Methods (==) :: Qual -> Qual -> Bool # (/=) :: Qual -> Qual -> Bool #
Integral Qual #
Methods quot :: Qual -> Qual -> Qual # rem :: Qual -> Qual -> Qual # div :: Qual -> Qual -> Qual # mod :: Qual -> Qual -> Qual # quotRem :: Qual -> Qual -> (Qual, Qual) # divMod :: Qual -> Qual -> (Qual, Qual) # toInteger :: Qual -> Integer #
Num Qual #
Methods (+) :: Qual -> Qual -> Qual # (-) :: Qual -> Qual -> Qual # (*) :: Qual -> Qual -> Qual # negate :: Qual -> Qual # abs :: Qual -> Qual # signum :: Qual -> Qual # fromInteger :: Integer -> Qual #
Ord Qual #
Methods compare :: Qual -> Qual -> Ordering # (<) :: Qual -> Qual -> Bool # (<=) :: Qual -> Qual -> Bool # (>) :: Qual -> Qual -> Bool # (>=) :: Qual -> Qual -> Bool # max :: Qual -> Qual -> Qual # min :: Qual -> Qual -> Qual #
Real Qual #
Methods toRational :: Qual -> Rational #
Show Qual #
Methods showsPrec :: Int -> Qual -> ShowS # show :: Qual -> String # showList :: [Qual] -> ShowS #

newtype Offset #

An Offset is a zero-based index into a sequence

Constructors

Offset
Fields unOff :: Int64

Instances

Enum Offset #
Methods succ :: Offset -> Offset # pred :: Offset -> Offset # toEnum :: Int -> Offset # fromEnum :: Offset -> Int # enumFrom :: Offset -> [Offset] # enumFromThen :: Offset -> Offset -> [Offset] # enumFromTo :: Offset -> Offset -> [Offset] # enumFromThenTo :: Offset -> Offset -> Offset -> [Offset] #
Eq Offset #
Methods (==) :: Offset -> Offset -> Bool # (/=) :: Offset -> Offset -> Bool #
Integral Offset #
Methods quot :: Offset -> Offset -> Offset # rem :: Offset -> Offset -> Offset # div :: Offset -> Offset -> Offset # mod :: Offset -> Offset -> Offset # quotRem :: Offset -> Offset -> (Offset, Offset) # divMod :: Offset -> Offset -> (Offset, Offset) # toInteger :: Offset -> Integer #
Num Offset #
Methods (+) :: Offset -> Offset -> Offset # (-) :: Offset -> Offset -> Offset # (*) :: Offset -> Offset -> Offset # negate :: Offset -> Offset # abs :: Offset -> Offset # signum :: Offset -> Offset # fromInteger :: Integer -> Offset #
Ord Offset #
Methods compare :: Offset -> Offset -> Ordering # (<) :: Offset -> Offset -> Bool # (<=) :: Offset -> Offset -> Bool # (>) :: Offset -> Offset -> Bool # (>=) :: Offset -> Offset -> Bool # max :: Offset -> Offset -> Offset # min :: Offset -> Offset -> Offset #
Real Offset #
Methods toRational :: Offset -> Rational #
Show Offset #
Methods showsPrec :: Int -> Offset -> ShowS # show :: Offset -> String # showList :: [Offset] -> ShowS #

newtype SeqData #

Sequence data are lazy bytestrings of ASCII characters.

Constructors

SeqData
Fields unSD :: ByteString

Instances

Eq SeqData #
Methods (==) :: SeqData -> SeqData -> Bool # (/=) :: SeqData -> SeqData -> Bool #
Ord SeqData #
Methods compare :: SeqData -> SeqData -> Ordering # (<) :: SeqData -> SeqData -> Bool # (<=) :: SeqData -> SeqData -> Bool # (>) :: SeqData -> SeqData -> Bool # (>=) :: SeqData -> SeqData -> Bool # max :: SeqData -> SeqData -> SeqData # min :: SeqData -> SeqData -> SeqData #
Show SeqData #
Methods showsPrec :: Int -> SeqData -> ShowS # show :: SeqData -> String # showList :: [SeqData] -> ShowS #
IsString SeqData #
Methods fromString :: String -> SeqData #
Monoid SeqData #
Methods mempty :: SeqData # mappend :: SeqData -> SeqData -> SeqData # mconcat :: [SeqData] -> SeqData #
Stringable SeqData #
Methods toString :: SeqData -> String # fromString :: String -> SeqData # length :: SeqData -> Int # toText :: SeqData -> Text # fromText :: Text -> SeqData # toLazyText :: SeqData -> Text # fromLazyText :: Text -> SeqData # toByteString :: SeqData -> ByteString # fromByteString :: ByteString -> SeqData # toLazyByteString :: SeqData -> ByteString # fromLazyByteString :: ByteString -> SeqData # toFilePath :: SeqData -> FilePath # fromFilePath :: FilePath -> SeqData #

newtype SeqLabel #

Sequence data are lazy bytestrings of ASCII characters.

Constructors

SeqLabel
Fields unSL :: ByteString

Instances

Eq SeqLabel #
Methods (==) :: SeqLabel -> SeqLabel -> Bool # (/=) :: SeqLabel -> SeqLabel -> Bool #
Ord SeqLabel #
Methods compare :: SeqLabel -> SeqLabel -> Ordering # (<) :: SeqLabel -> SeqLabel -> Bool # (<=) :: SeqLabel -> SeqLabel -> Bool # (>) :: SeqLabel -> SeqLabel -> Bool # (>=) :: SeqLabel -> SeqLabel -> Bool # max :: SeqLabel -> SeqLabel -> SeqLabel # min :: SeqLabel -> SeqLabel -> SeqLabel #
Show SeqLabel #
Methods showsPrec :: Int -> SeqLabel -> ShowS # show :: SeqLabel -> String # showList :: [SeqLabel] -> ShowS #
IsString SeqLabel #
Methods fromString :: String -> SeqLabel #
Monoid SeqLabel #
Methods mempty :: SeqLabel # mappend :: SeqLabel -> SeqLabel -> SeqLabel # mconcat :: [SeqLabel] -> SeqLabel #
Stringable SeqLabel #
Methods toString :: SeqLabel -> String # fromString :: String -> SeqLabel # length :: SeqLabel -> Int # toText :: SeqLabel -> Text # fromText :: Text -> SeqLabel # toLazyText :: SeqLabel -> Text # fromLazyText :: Text -> SeqLabel # toByteString :: SeqLabel -> ByteString # fromByteString :: ByteString -> SeqLabel # toLazyByteString :: SeqLabel -> ByteString # fromLazyByteString :: ByteString -> SeqLabel # toFilePath :: SeqLabel -> FilePath # fromFilePath :: FilePath -> SeqLabel #

newtype QualData #

Quality data are lazy bytestrings of Quals.

Constructors

QualData
Fields unQD :: ByteString

Instances

Eq QualData #
Methods (==) :: QualData -> QualData -> Bool # (/=) :: QualData -> QualData -> Bool #
Ord QualData #
Methods compare :: QualData -> QualData -> Ordering # (<) :: QualData -> QualData -> Bool # (<=) :: QualData -> QualData -> Bool # (>) :: QualData -> QualData -> Bool # (>=) :: QualData -> QualData -> Bool # max :: QualData -> QualData -> QualData # min :: QualData -> QualData -> QualData #
Show QualData #
Methods showsPrec :: Int -> QualData -> ShowS # show :: QualData -> String # showList :: [QualData] -> ShowS #
Monoid QualData #
Methods mempty :: QualData # mappend :: QualData -> QualData -> QualData # mconcat :: [QualData] -> QualData #
Stringable QualData #
Methods toString :: QualData -> String # fromString :: String -> QualData # length :: QualData -> Int # toText :: QualData -> Text # fromText :: Text -> QualData # toLazyText :: QualData -> Text # fromLazyText :: Text -> QualData # toByteString :: QualData -> ByteString # fromByteString :: ByteString -> QualData # toLazyByteString :: QualData -> ByteString # fromLazyByteString :: ByteString -> QualData # toFilePath :: QualData -> FilePath # fromFilePath :: FilePath -> QualData #

Class definitions

class BioSeq s where #

The BioSeq class models sequence data, and any data object that represents a biological sequence should implement it.

Minimal complete definition

seqdata, seqlength

Methods

seqid :: s -> SeqLabel #

seqheader :: s -> SeqLabel #

seqdata :: s -> SeqData #

seqlength :: s -> Offset #

seqlabel :: s -> SeqLabel #

Deprecated: Warning: seqlabel is deprecated, use seqid or seqheader instead.

class BioSeq sq => BioSeqQual sq where #

The BioSeqQual class extends BioSeq with quality data. Any correspondig data object should be an instance, this will allow Fasta formatted quality data toFastaQual, as well as the combined FastQ format (via toFastQ).

Minimal complete definition

seqqual

Methods

seqqual :: sq -> QualData #

Helper functions

toFasta :: BioSeq s => s -> ByteString #

Any BioSeq can be formatted as Fasta, 60-char lines.

toFastaQual :: BioSeqQual s => s -> ByteString #

Output Fasta-formatted quality data (.qual files), where quality values are output as whitespace-separated integers.

toFastQ :: BioSeqQual s => s -> ByteString #

Output FastQ-formatted data. For simplicity, only the Sanger quality format is supported, and only four lines per sequence (i.e. no line breaks in sequence or quality data).

module Data.Stringable