bio-0.4.4: 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 2.6.1