Bio.FASTA.Type

Documentation

type Fasta a = [FastaItem a]

Type alias for FASTA file. satisfies the following format : >(s|t)*[^nr]+(s|t)*(n|r)*((w|s)(n|r)*)*

data FastaItem a

One record in FASTA file.

Constructors

FastaItem

Fields

• name :: Text

  name of the sequence

• sequ :: BareSequence a

  bare sequence

Instances

Functor FastaItem

Defined in Bio.FASTA.Type

Methods

fmap :: (a -> b) -> FastaItem a -> FastaItem b

(<$) :: a -> FastaItem b -> FastaItem a

Eq a => Eq (FastaItem a)

Defined in Bio.FASTA.Type

Methods

(==) :: FastaItem a -> FastaItem a -> Bool

(/=) :: FastaItem a -> FastaItem a -> Bool

Show a => Show (FastaItem a)

Defined in Bio.FASTA.Type

Methods

showsPrec :: Int -> FastaItem a -> ShowS

show :: FastaItem a -> String

showList :: [FastaItem a] -> ShowS

class ParsableFastaToken a where

Methods

parseToken :: (Char -> Bool) -> Parser a

Instances

ParsableFastaToken Char

Defined in Bio.FASTA.Parser

Methods

parseToken :: (Char -> Bool) -> Parser Char

ParsableFastaToken ModItem

Defined in Bio.FASTA.Parser

Methods

parseToken :: (Char -> Bool) -> Parser ModItem

data Modification

Constructors

Mod_A_Star

Mod_C_Star

Mod_G_Star

Mod_T_Star

Mod_rA

Mod_rC

Mod_rG

Mod_rU

Mod_Plus_A

Mod_Plus_C

Mod_Plus_G

Mod_Plus_T

Mod_rAf

Mod_rCf

Mod_rGf

Mod_rUf

Mod_mA

Mod_mC

Mod_mG

Mod_mU

Mod_mA_Star

Mod_mC_Star

Mod_mG_Star

Mod_mU_Star

Mod_dU

Mod_5Bio

Mod_iBio

Mod_56FAM

Mod_36FAM

Mod_5HEX

Mod_5TMR

Mod_3BHQ1

Mod_3BHQ2

Mod_5NH2

Mod_3NH2

Mod_5PO4

Mod_3PO4

Mod_3BioTEG

Mod_C12

Mod_NHSdT

Mod_5Mal

Mod_5thio

Mod_3thio

Mod_3azide

Mod_3alkine

Mod_5CholTEG

Mod_3CholTEG

Mod_5C10

Mod_5Alk

Mod_GC

Mod_GT

Mod_AT

Mod_TG

Mod_AC

Mod_CC

Mod_AA

Mod_TC

Mod_TT

Mod_CG

Mod_GG

Mod_AG

Mod_GA

Mod_CA

Mod_CT

Mod_TA

Mod_AAA

Mod_AAC

Mod_ACT

Mod_ATC

Mod_ATG

Mod_CAG

Mod_AGA

Mod_CAT

Mod_CCG

Mod_CGT

Mod_CTG

Mod_GAA

Mod_GAC

Mod_GCT

Mod_GGT

Mod_GTT

Mod_TAC

Mod_TCT

Mod_TGC

Mod_TGG

Mod_TTC

Mod_TTT

Unknown String

Instances

Eq Modification

Defined in Bio.FASTA.Type

Methods

(==) :: Modification -> Modification -> Bool

(/=) :: Modification -> Modification -> Bool

Show Modification

Defined in Bio.FASTA.Type

Methods

showsPrec :: Int -> Modification -> ShowS

show :: Modification -> String

showList :: [Modification] -> ShowS

data ModItem

Constructors

Mod Modification

Letter Char

Instances

Eq ModItem

Defined in Bio.FASTA.Type

Methods

(==) :: ModItem -> ModItem -> Bool

(/=) :: ModItem -> ModItem -> Bool

Show ModItem

Defined in Bio.FASTA.Type

Methods

showsPrec :: Int -> ModItem -> ShowS

show :: ModItem -> String

showList :: [ModItem] -> ShowS

ParsableFastaToken ModItem

Defined in Bio.FASTA.Parser

Methods

parseToken :: (Char -> Bool) -> Parser ModItem

WritableFastaToken ModItem

Defined in Bio.FASTA.Writer

Methods

tokenToString :: ModItem -> String

modificationToString :: Modification -> String