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Bio.Location.SeqLocation
Contents
Positions on named sequences Contiguous location spans on named sequences Arbitrary location spans on named sequences Testing for location intersection on named sequences Extracting subsequences Displaying locations on named sequences
Description
Data types for sequence locations and sequence positions associated with specific, named sequences.
Synopsis
type SeqPos = OnSeq Pos
type ContigSeqLoc = OnSeq ContigLoc
withinContigSeqLoc :: SeqPos -> ContigSeqLoc -> Bool
type SeqLoc = OnSeq Loc
isWithin :: SeqPos -> SeqLoc -> Bool
overlaps :: SeqLoc -> SeqLoc -> Bool
seqData :: (Error e, MonadError e m) => (SeqName -> m SeqData) -> SeqLoc -> m SeqData
displaySeqPos :: SeqPos -> String
displayContigSeqLoc :: ContigSeqLoc -> String
display :: SeqLoc -> String
Positions on named sequences
type SeqPos = OnSeq Pos | Source
A position on a named sequence
Contiguous location spans on named sequences
type ContigSeqLoc = OnSeq ContigLoc | Source
A location consisting of a contiguous span of positions on a named sequence.
withinContigSeqLoc :: SeqPos -> ContigSeqLoc -> Bool | Source
Test whether a sequence position lies within a sequence location. This requires that the position lie within the location as per `isWithin` and have the same sequence name.
Arbitrary location spans on named sequences
type SeqLoc = OnSeq Loc | Source
A general location, consisting of spans of sequence positions on a specific, named sequence.
Testing for location intersection on named sequences
isWithin :: SeqPos -> SeqLoc -> Bool | Source
Test whether a sequence position lies within a sequence location. This requires that the position lie within the location as per `isWithin` and have the same sequence name.
overlaps :: SeqLoc -> SeqLoc -> Bool | Source
Test whether two sequence locations overlap in any position. This requires that the locations overlap as per `overlaps` and have the same sequence name.
Extracting subsequences
seqData :: (Error e, MonadError e m) => (SeqName -> m SeqData) -> SeqLoc -> m SeqData | Source
Extract the subsequence specified by a sequence location from a sequence database. The sequence name is used to retrieve the full sequence and the subsequence is extracted as by `seqData`
Displaying locations on named sequences
displaySeqPos :: SeqPos -> String | Source
Display a human-friendly representation of a `SeqPos`
displayContigSeqLoc :: ContigSeqLoc -> String | Source
Display a human-friendly representation of a `ContigSeqLoc`
display :: SeqLoc -> String | Source
Display a human-friendly representation of a `SeqLoc`
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