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Bio.Location.ContigLocation

Contents

Sequence locations
Locations and positions
Extracting subsequences
Transforming locations
Displaying locations

Description
Data type for a sequence location consiting of a contiguous range of positions on the sequence. Throughout, sequence position refers to a `Pos` which includes a strand. An index into a sequence is referred to as an offset, and is generally of type `Offset`.
Synopsis

data ContigLoc = ContigLoc {

offset5 :: !Offset
length :: !Offset
strand :: !Strand

}

fromStartEnd :: Offset -> Offset -> ContigLoc
fromPosLen :: Pos -> Offset -> ContigLoc
bounds :: ContigLoc -> (Offset, Offset)
startPos :: ContigLoc -> Pos
endPos :: ContigLoc -> Pos
posInto :: Pos -> ContigLoc -> Maybe Pos
posOutof :: Pos -> ContigLoc -> Maybe Pos
isWithin :: Pos -> ContigLoc -> Bool
overlaps :: ContigLoc -> ContigLoc -> Bool
seqData :: (Error e, MonadError e m) => SeqData -> ContigLoc -> m SeqData
seqDataPadded :: SeqData -> ContigLoc -> SeqData
slide :: Offset -> ContigLoc -> ContigLoc
extend :: (Offset, Offset) -> ContigLoc -> ContigLoc
display :: ContigLoc -> String

Sequence locations

data ContigLoc | Source

Contiguous sequence location defined by a span of sequence positions, lying on a specific strand of the sequence.
Constructors

ContigLoc |

offset5 :: !Offset | The offset of the 5' end of the location, as a 0-based index
length :: !Offset | The length of the location
strand :: !Strand | The strand of the location

Instances

Eq ContigLoc
Ord ContigLoc
Show ContigLoc
Stranded ContigLoc

fromStartEnd :: Offset -> Offset -> ContigLoc | Source

Create a sequence location lying between 0-based starting and ending offsets. When `start < end`, the location be on the forward strand, otherwise it will be on the reverse complement strand.

fromPosLen :: Pos -> Offset -> ContigLoc | Source

Create a sequence location from the sequence position of the start of the location and the length of the position. The strand of the location, and the direction it extends from the starting position, are determined by the strand of the starting position.
Locations and positions

bounds :: ContigLoc -> (Offset, Offset) | Source

The bounds of a sequence location. This is a pair consisting of the lowest and highest sequence offsets covered by the region. The bounds ignore the strand of the sequence location, and the first element of the pair will always be lower than the second.

startPos :: ContigLoc -> Pos | Source

Sequence position of the start of the location. This is the 5' end on the location strand, which will have a higher offset than `endPos` if the location is on the `RevCompl` strand.

endPos :: ContigLoc -> Pos | Source

Sequence position of the end of the location, as described in `startPos`.

posInto :: Pos -> ContigLoc -> Maybe Pos | Source

Given a sequence position and a sequence location relative to the same sequence, compute a new position representing the original position relative to the subsequence defined by the location. If the sequence position lies outside of the sequence location, `Nothing` is returned; thus, the offset of the new position will always be in the range `[0, length cloc - 1]`.

posOutof :: Pos -> ContigLoc -> Maybe Pos | Source

Given a sequence location and a sequence position within that location, compute a new position representing the original position relative to the outer sequence. If the sequence position lies outside the location, `Nothing` is returned. This function inverts `posInto` when the sequence position lies within the position is actually within the location.

isWithin :: Pos -> ContigLoc -> Bool | Source

Returns `True` when a sequence position lies within a sequence location on the same sequence, and occupies the same strand.

overlaps :: ContigLoc -> ContigLoc -> Bool | Source

Returns `True` when two sequence locations overlap at any position.
Extracting subsequences

seqData :: (Error e, MonadError e m) => SeqData -> ContigLoc -> m SeqData | Source

Extract the nucleotide `SeqData` for the sequence location. If any part of the location lies outside the bounds of the sequence, an error results.

seqDataPadded :: SeqData -> ContigLoc -> SeqData | Source

As `seqData`, extract the nucleotide subsequence for the location. Any positions in the location lying outside the bounds of the sequence are returned as `N` rather than producing an error.
Transforming locations

slide :: Offset -> ContigLoc -> ContigLoc | Source

Returns a location resulting from sliding the original location along the sequence by a specified offset. A positive offset will move the location away from the 5' end of the forward stand of the sequence regardless of the strand of the location itself. Thus,

     slide (revCompl cloc) off == revCompl (slide cloc off)

extend :: (Offset, Offset) -> ContigLoc -> ContigLoc | Source

Returns a sequence location produced by extending the original location on each end, based on a pair of (5\' extension, /3' extension/). The 5' extension is applied to the 5' end of the location on the location strand; if the location is on the `RevCompl` strand, the 5' end will have a higher offset than the 3' end and this offset will increase by the amount of the 5' extension. Similarly, the 3' extension is applied to the 3' end of the location.

Displaying locations

display :: ContigLoc -> String | Source

Display a human-friendly, zero-based representation of a sequence location.
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