Bio.SeqLoc.Location

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, as opposed to an offset, which refers to a Offset with no strand.

Sequence locations

class Location l where

Methods

strand :: l -> Strand

length :: l -> Offset

bounds :: l -> (Offset, Offset)

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 :: l -> Pos

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 Minus strand.

endPos :: l -> Pos

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

allPos :: l -> [Pos]

List of sequence positions in the location, in order from the 5' end to the 3' end of the location strand.

seqData :: (SeqLike s, Stranded s) => s -> l -> Maybe s

Extract Just the nucleotide SeqLike for the sequence location, or Nothing if f any part of the location lies outside the bounds of the sequence.

seqDataPad :: (SeqLike s, Stranded s) => s -> l -> s

As seqData, extract the nucleotide subsequence for the location, but any positions in the location lying outside the bounds of the sequence are returned as N.

posInto :: Pos -> l -> Maybe Pos

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 l - 1].

posOutof :: Pos -> l -> Maybe Pos

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.

clocInto :: ContigLoc -> l -> Maybe ContigLoc

For an enclosing location and a sublocation in the same coordinate system, find the image of the sublocation relative to the enclosing location. For example, if the enclosing location spans (100, 150) and the sublocation is (110, 120) then clocInto will be (10, 20).

clocOutof :: ContigLoc -> l -> Maybe l

Returns a sequence location produced by finding the inverse image of a sublocation, with coordinates given relative to an enclosing location, in the coordinate system of the enclosing location. For example, if the enclosing location spans (100, 150) and the sublocation is (10, 20) then clocOutof will be (110, 120).

extend :: (Offset, Offset) -> l -> l

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 Minus 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.

offsetWithin :: Offset -> l -> Bool

Returns True when a sequence offset lies within a sequence location on the same sequence

posWithin :: Pos -> l -> Bool

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

contigOverlaps :: ContigLoc -> l -> Bool

Returns True when two sequence locations overlap at any position.

toContigs :: l -> [ContigLoc]

Contigs that comprise the location

Instances

Location ContigLoc

Location SpliceLoc

overlaps :: (Location l1, Location l2) => l1 -> l2 -> Bool

Contiguous sequence locations

data ContigLoc

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

Instances

Eq ContigLoc

Ord ContigLoc

Show ContigLoc

LocRepr ContigLoc

Stranded ContigLoc

Location ContigLoc

Locatable ContigSeqLoc

offset5 :: ContigLoc -> Offset

The offset of the 5' end of the location, as a 0-based index

fromStartEnd :: Offset -> Offset -> ContigLoc

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

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.

fromBoundsStrand :: Offset -> Offset -> Strand -> ContigLoc

Create a sequence location between 0-based starting and ending bounds with a specified strand.

Transforming locations

slide :: Offset -> ContigLoc -> ContigLoc

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)