package biotk

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in-package search v0.2.0

package biotk

biotk
- Biotk
  - Bai
  - Bam_iterator
  - Bed
    
    Bed3
    
    Record
    
    Bed4
    
    Record
    
    Bed5
    
    Record
    
    Bed6
    
    Record
    
    Record
    
    S
  - Cisbp
    
    Motif
    
    TF_information
  - Dataframe
    
    Ez
  - Dna_sequence
    
    Parser
    
    Parser_of_char
    
    P
  - Encode
    
    Experiment_list
  - Fasta
  - Fastq
    
    Stats
  - FeatureCounts
    
    Summary
    
    Tsv
    
    Fields
    
    Direct
  - GAnnot
    
    LAssoc
    
    LMap
    
    LSet
    
    Selection
  - GLoc
    
    Map
    
    Key
    
    Provide_hash
    
    Provide_of_sexp
    
    Key
    
    Tree
    
    Provide_of_sexp
    
    K
    
    Set
    
    Elt
    
    Named
    
    Provide_hash
    
    Provide_of_sexp
    
    Elt
    
    Tree
    
    Named
    
    Provide_of_sexp
    
    Elt
  - Gcf
  - Gene
    
    Transcript
  - Gff
    
    Item
    
    Record
  - Gtf
    
    Annotation
    
    Item
    
    Record
  - Idr
    
    Broad_output
    
    Row
    
    Narrow_output
    
    Row
  - Igv
    
    Statement
    
    proxy
  - Interval_union
  - Jaspar
  - Let_syntax
    
    Result
  - Line_oriented
    
    Item
    
    Make
    
    Item
    
    S
  - List1
  - Macs
    
    Xls
  - Macs2
    
    Broad_peaks
    
    Xls
  - Misc
  - NarrowPeak
    
    Item
  - Ncbi_genome
    
    Assembly_summary
  - Nucleotide
  - Phylo_tree_draw
  - Pipe_parsers
    
    Monad_infix
  - Profile_matrix
    
    Alphabet
    
    DNA
    
    Make
    
    A
    
    S
  - Pwm
  - Pwm_stats
    
    TFM_pvalue
  - Range
  - Sam
  - Ucsc_genome_browser
    
    Chrom_size
    
    Fields
    
    Direct
  - Utils
  - Wfa
    
    Make
    
    Profile
    
    Score
    
    Symbol
    
    Nucleotide
    
    Nucleotide_IUPAC
    
    Nucleotide_frequency
    
    PSSM
    
    Profile
    
    S
    
    Score
    
    Symbol
biotk.croquis
- Biotk_croquis
biotk.pipes
- Biotk_pipes
  - Pipe
    
    Make
    
    M
    
    Monad_infix
    
    Monad
    
    S
    
    Monad_infix
biotk.pipes.unix
- Biotk_pipes_unix
  - Pipe
    
    Monad_infix

Legend:
Library
Module
Module type
Parameter
Class
Class type

A set of locations (e.g. a set of gene loci)

type t

val empty : t

val to_stream : t -> GLoc.t Stream.t

val of_stream : GLoc.t Stream.t -> t

val intersects : t -> GLoc.t -> bool

intersects lset loc returns true if loc has a non-empty intersection with one of the locations in lset, and returns false otherwise

val closest : t -> GLoc.t -> (GLoc.t * int) option

closest lset loc returns the GLoc.t in lset that is the closest to loc, along with the actual (minimal) distance. Returns None if there is no GLoc.t in lset that comes from the same chromosome than loc.

val intersecting_elems : t -> GLoc.t -> GLoc.t Stream.t

intersecting_elems lset loc returns a stream of all locations in lset that intersect loc.