| bio-0.4: A bioinformatics library | Source code | Contents | Index

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`
Produced by Haddock version 2.4.2