Biobase.Types.Location

Annotate the genomic Location of features or elements. A Location is always contiguous, using strand, 0-based position, and length. Transformation to different systems of annotation is made possible.

Documentation

class ModifyLocation posTy seqTy where

Operations on locations.

Methods

locAppendLeft :: seqTy -> Location i posTy seqTy -> Location i posTy seqTy

Append to the left.

locAppendRight :: seqTy -> Location i posTy seqTy -> Location i posTy seqTy

Append to the right.

locSplitAt :: Int -> Location i posTy seqTy -> (Location i posTy seqTy, Location i posTy seqTy)

Split a location.

locLength :: Location i posTy seqTy -> Int

Length of location

Instances

ModifyLocation FwdPosition Int

Defined in Biobase.Types.Location

Methods

locAppendLeft :: forall k (i :: k). Int -> Location i FwdPosition Int -> Location i FwdPosition Int

locAppendRight :: forall k (i :: k). Int -> Location i FwdPosition Int -> Location i FwdPosition Int

locSplitAt :: forall k (i :: k). Int -> Location i FwdPosition Int -> (Location i FwdPosition Int, Location i FwdPosition Int)

locLength :: forall k (i :: k). Location i FwdPosition Int -> Int

ModifyLocation FwdPosition (BioSequence w)

Defined in Biobase.Types.Location

Methods

locAppendLeft :: forall k (i :: k). BioSequence w -> Location i FwdPosition (BioSequence w) -> Location i FwdPosition (BioSequence w)

locAppendRight :: forall k (i :: k). BioSequence w -> Location i FwdPosition (BioSequence w) -> Location i FwdPosition (BioSequence w)

locSplitAt :: forall k (i :: k). Int -> Location i FwdPosition (BioSequence w) -> (Location i FwdPosition (BioSequence w), Location i FwdPosition (BioSequence w))

locLength :: forall k (i :: k). Location i FwdPosition (BioSequence w) -> Int

locTake :: forall k posTy seqTy (i :: k). ModifyLocation posTy seqTy => Int -> Location i posTy seqTy -> Location i posTy seqTy

locTakeEnd :: forall k posTy seqTy (i :: k). ModifyLocation posTy seqTy => Int -> Location i posTy seqTy -> Location i posTy seqTy

locDrop :: forall k posTy seqTy (i :: k). ModifyLocation posTy seqTy => Int -> Location i posTy seqTy -> Location i posTy seqTy

locDropEnd :: forall k posTy seqTy (i :: k). ModifyLocation posTy seqTy => Int -> Location i posTy seqTy -> Location i posTy seqTy

locSplitEndAt :: forall k posTy seqTy (i :: k). ModifyLocation posTy seqTy => Int -> Location i posTy seqTy -> (Location i posTy seqTy, Location i posTy seqTy)

data Location ident posTy seqTy

Constructors

Location

Fields

• _locIdentifier :: !(SequenceIdentifier ident)
• _locPosition :: !posTy
• _locSequence :: !seqTy

Instances

(Typeable ident, Typeable k, Data posTy, Data seqTy) => Data (Location ident posTy seqTy)

Defined in Biobase.Types.Location

Methods

gfoldl :: (forall d b. Data d => c (d -> b) -> d -> c b) -> (forall g. g -> c g) -> Location ident posTy seqTy -> c (Location ident posTy seqTy)

gunfold :: (forall b r. Data b => c (b -> r) -> c r) -> (forall r. r -> c r) -> Constr -> c (Location ident posTy seqTy)

toConstr :: Location ident posTy seqTy -> Constr

dataTypeOf :: Location ident posTy seqTy -> DataType

dataCast1 :: Typeable t => (forall d. Data d => c (t d)) -> Maybe (c (Location ident posTy seqTy))

dataCast2 :: Typeable t => (forall d e. (Data d, Data e) => c (t d e)) -> Maybe (c (Location ident posTy seqTy))

gmapT :: (forall b. Data b => b -> b) -> Location ident posTy seqTy -> Location ident posTy seqTy

gmapQl :: (r -> r' -> r) -> r -> (forall d. Data d => d -> r') -> Location ident posTy seqTy -> r

gmapQr :: forall r r'. (r' -> r -> r) -> r -> (forall d. Data d => d -> r') -> Location ident posTy seqTy -> r

gmapQ :: (forall d. Data d => d -> u) -> Location ident posTy seqTy -> [u]

gmapQi :: Int -> (forall d. Data d => d -> u) -> Location ident posTy seqTy -> u

gmapM :: Monad m => (forall d. Data d => d -> m d) -> Location ident posTy seqTy -> m (Location ident posTy seqTy)

gmapMp :: MonadPlus m => (forall d. Data d => d -> m d) -> Location ident posTy seqTy -> m (Location ident posTy seqTy)

gmapMo :: MonadPlus m => (forall d. Data d => d -> m d) -> Location ident posTy seqTy -> m (Location ident posTy seqTy)

(Show posTy, Show seqTy) => Show (Location ident posTy seqTy)

Defined in Biobase.Types.Location

Methods

showsPrec :: Int -> Location ident posTy seqTy -> ShowS

show :: Location ident posTy seqTy -> String

showList :: [Location ident posTy seqTy] -> ShowS

Generic (Location ident posTy seqTy)

Defined in Biobase.Types.Location

Associated Types

type Rep (Location ident posTy seqTy) :: Type -> Type

Methods

from :: Location ident posTy seqTy -> Rep (Location ident posTy seqTy) x

to :: Rep (Location ident posTy seqTy) x -> Location ident posTy seqTy

Info (BioSequence w) => Info (Location i FwdPosition (BioSequence w))

Defined in Biobase.Types.Location

Methods

info :: Location i FwdPosition (BioSequence w) -> String

(NFData p, NFData s) => NFData (Location i p s)

Defined in Biobase.Types.Location

Methods

rnf :: Location i p s -> ()

Reversing (Location i FwdPosition (BioSequence w))

Defined in Biobase.Types.Location

Methods

reversing :: Location i FwdPosition (BioSequence w) -> Location i FwdPosition (BioSequence w)

Complement (BioSequence w) => Complement (Location i FwdPosition (BioSequence w))

Defined in Biobase.Types.Location

Methods

complement :: Iso' (Location i FwdPosition (BioSequence w)) (Location i FwdPosition (BioSequence w))

type Rep (Location ident posTy seqTy)

Defined in Biobase.Types.Location

type Rep (Location ident posTy seqTy) = D1 ('MetaData "Location" "Biobase.Types.Location" "BiobaseTypes-0.2.1.0-KNWEaQoA0aY419BnftjfF1" 'False) (C1 ('MetaCons "Location" 'PrefixI 'True) (S1 ('MetaSel ('Just "_locIdentifier") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 (SequenceIdentifier ident)) :*: (S1 ('MetaSel ('Just "_locPosition") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 posTy) :*: S1 ('MetaSel ('Just "_locSequence") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 seqTy))))

locSequence :: forall k (ident :: k) posTy seqTy seqTy. Lens (Location (ident :: k) posTy seqTy) (Location (ident :: k) posTy seqTy) seqTy seqTy

locPosition :: forall k (ident :: k) posTy seqTy posTy. Lens (Location (ident :: k) posTy seqTy) (Location (ident :: k) posTy seqTy) posTy posTy

locIdentifier :: forall k (ident :: k) posTy seqTy k (ident :: k). Lens (Location (ident :: k) posTy seqTy) (Location (ident :: k) posTy seqTy) (SequenceIdentifier ident) (SequenceIdentifier ident)

retagLocation :: Location i posTy seqTy -> Location j posTy seqTy

subLocation :: Location i FwdPosition (BioSequence w) -> (FwdPosition, Int) -> Location i FwdPosition (BioSequence w)

Will extract a substring for a given biosequence. It is allowed to hand in partially or not at all overlapping locational information. This will yield empty resulting locations.

This will convert the FwdPosition strand, which in turn allows dealing with reverse-complement searches.

0123456789
   3.3

data PIS i p s

Constructors

PIS

Fields

• _pisPrefix :: Maybe (Location i p s)
• _pisInfix :: !(Location i p s)
• _pisSuffix :: Maybe (Location i p s)

Instances

(Typeable i, Typeable k, Data p, Data s) => Data (PIS i p s)

Defined in Biobase.Types.Location

Methods

gfoldl :: (forall d b. Data d => c (d -> b) -> d -> c b) -> (forall g. g -> c g) -> PIS i p s -> c (PIS i p s)

gunfold :: (forall b r. Data b => c (b -> r) -> c r) -> (forall r. r -> c r) -> Constr -> c (PIS i p s)

toConstr :: PIS i p s -> Constr

dataTypeOf :: PIS i p s -> DataType

dataCast1 :: Typeable t => (forall d. Data d => c (t d)) -> Maybe (c (PIS i p s))

dataCast2 :: Typeable t => (forall d e. (Data d, Data e) => c (t d e)) -> Maybe (c (PIS i p s))

gmapT :: (forall b. Data b => b -> b) -> PIS i p s -> PIS i p s

gmapQl :: (r -> r' -> r) -> r -> (forall d. Data d => d -> r') -> PIS i p s -> r

gmapQr :: forall r r'. (r' -> r -> r) -> r -> (forall d. Data d => d -> r') -> PIS i p s -> r

gmapQ :: (forall d. Data d => d -> u) -> PIS i p s -> [u]

gmapQi :: Int -> (forall d. Data d => d -> u) -> PIS i p s -> u

gmapM :: Monad m => (forall d. Data d => d -> m d) -> PIS i p s -> m (PIS i p s)

gmapMp :: MonadPlus m => (forall d. Data d => d -> m d) -> PIS i p s -> m (PIS i p s)

gmapMo :: MonadPlus m => (forall d. Data d => d -> m d) -> PIS i p s -> m (PIS i p s)

(Show p, Show s) => Show (PIS i p s)

Defined in Biobase.Types.Location

Methods

showsPrec :: Int -> PIS i p s -> ShowS

show :: PIS i p s -> String

showList :: [PIS i p s] -> ShowS

Reversing (Location i FwdPosition (BioSequence w)) => Reversing (PIS i FwdPosition (BioSequence w))

Defined in Biobase.Types.Location

Methods

reversing :: PIS i FwdPosition (BioSequence w) -> PIS i FwdPosition (BioSequence w)

Complement (BioSequence w) => Complement (PIS i FwdPosition (BioSequence w))

Defined in Biobase.Types.Location

Methods

complement :: Iso' (PIS i FwdPosition (BioSequence w)) (PIS i FwdPosition (BioSequence w))

pisSuffix :: forall k (i :: k) p s. Lens' (PIS (i :: k) p s) (Maybe (Location i p s))

pisPrefix :: forall k (i :: k) p s. Lens' (PIS (i :: k) p s) (Maybe (Location i p s))

pisInfix :: forall k (i :: k) p s. Lens' (PIS (i :: k) p s) (Location i p s)

pis :: forall k (i :: k) p s. Location i p s -> PIS i p s

retagPis :: PIS i p s -> PIS j p s

subPisLocation :: PIS i FwdPosition (BioSequence w) -> (FwdPosition, Int) -> PIS i FwdPosition (BioSequence w)

Given a PIS, this will return the substring indicated by the location in the 2nd argument. Allows for easy substring extraction, and retains the system of prefixinfixsuffix.

It is allowed to hand locations that only partially (or not at all) correspond to the PIS, but then the resulting PIS will be empty!

pisSequence :: Lens (PIS i p (BioSequence s)) (PIS i p (BioSequence t)) (BioSequence s) (BioSequence t)

locAsLength :: Location i FwdPosition (BioSequence w) -> Location i FwdPosition Int

Given a Location with a BioSequence, replace the sequence with its length.

blastRange1 :: Location i FwdPosition Int -> (Int, Int, Strand)

Provides a range in a notation as used by blast, for example. This isomorphism can translate back as well. FwdLocation - 8 4 ^. blastRange1 == 9 6 MinusStrand, since these ranges are 1-based and start and end included.

attachPrefixes :: (Monad m, ModifyLocation p s) => Int -> Stream (Of (PIS i p s)) m r -> Stream (Of (PIS i p s)) m r

For each element, attach the prefix as well. The Int indicates the maximal prefix length to attach.

1 2 3 4 -> 01 12 23 34

TODO are we sure this is correct for MinusStrand?

attachSuffixes :: (Monad m, ModifyLocation p s) => Int -> Stream (Of (PIS i p s)) m r -> Stream (Of (PIS i p s)) m r

For each element, attach the suffix as well.

1 2 3 4 -> 12 23 34 40