package biotk

You can search for identifiers within the package.

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
    
    Parser
  - Dna_sequence
    
    Parser
    
    Parser_of_char
    
    P
  - Encode
    
    Experiment_list
  - Fasta
  - Fastq
    
    Stats
  - FeatureCounts
    
    Summary
    
    Tsv
    
    Fields
    
    Direct
  - GAnnot
    
    LAssoc
    
    LMap
    
    LSet
    
    Selection
  - GLoc
  - 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
  - RanT
  - 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
  - Croquis
    
    Font
    
    Layout
    
    Picture
    
    Plot
    
    Scaling
    
    Viewport
  - Font_data
    
    Internal
  - Vg_text
    
    Font
    
    Layout
biotk.pipes
- Biotk_pipes
  - Pipe
    
    Make
    
    M
    
    Monad_infix
    
    Monad
    
    S
    
    Monad_infix
biotk.pipes.unix
- Biotk_pipes_unix
  - Pipe
    
    Monad_infix

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Class type

include module type of Biotk_pipes_unix.Pipe

include Biotk_pipes.Pipe.S with type 'a monad = 'a

type 'a monad = 'a

type 'a thunk = unit -> 'a

type finalizer = (unit -> unit monad) option

type ('i, 'o, 'r) t =

| Has_output of 'o * ('i, 'o, 'r) t thunk * finalizer
| Needs_input of 'i option -> ('i, 'o, 'r) t
| Done of 'r
| PipeM of ('i, 'o, 'r) t monad thunk

type 'a source = (Biotk_pipes.Pipe.void, 'a, unit) t

type 'a sink = ('a, Biotk_pipes.Pipe.void, unit) t

val return : 'r -> (_, _, 'r) t

val bind : ('i, 'o, 'a) t -> ('a -> ('i, 'o, 'b) t) -> ('i, 'o, 'b) t

module Monad_infix : sig ... end

val await : unit -> ('a, _, 'a option) t

val yield : 'o -> (_, 'o, unit) t

val compose : ('i, 'a, _) t -> ('a, 'o, 'r) t -> ('i, 'o, 'r) t

val ($$) : ('i, 'a, _) t -> ('a, 'o, 'r) t -> ('i, 'o, 'r) t

val run : (Biotk_pipes.Pipe.void, Biotk_pipes.Pipe.void, 'r) t -> 'r monad

val bracket : 
  (unit -> 'a monad) ->
  ('a -> unit monad) ->
  ('a -> ('i, 'o, 'r) t) ->
  ('i, 'o, 'r) t

val fold : 'r -> ('i -> 'r -> 'r) -> ('i, Biotk_pipes.Pipe.void, 'r) t

val map : ('i -> 'o) -> ('i, 'o, unit) t

val mapi : (int -> 'i -> 'o) -> ('i, 'o, unit) t

val filter : ('i -> bool) -> ('i, 'i, unit) t

val filter_map : ('i -> 'o option) -> ('i, 'o, unit) t

val from_list : 'a list -> 'a source

val to_list : unit -> ('a, Biotk_pipes.Pipe.void, 'a list) t

val all : 
  unit ->
  (('a, 'b) Stdlib.result, Biotk_pipes.Pipe.void, ('a list, 'b) Stdlib.result)
    t

val loop : ('a -> 'b option -> 'a * 'c list) -> 'a -> ('b, 'c, unit) t

val loop' : 
  ('a -> 'b option -> ('a * 'c list, 'd) Stdlib.result) ->
  'a ->
  ('b, 'c, (unit, 'd) Stdlib.result) t

val drop : int -> ('a, 'a, unit) t

val from_file : ?buffer_size:int -> string -> string source

val to_file : string -> string sink

val lines : unit -> (string, Biocaml_base.Line.t, unit) t

val lines_to_strings : unit -> (Biocaml_base.Line.t, string, unit) t

val bed_parser : unit -> (string, Biocaml_base.Bed.item, unit) t

val bed_unparser : unit -> (Biocaml_base.Bed.item, string, unit) t

val gff3_parser : unit -> (string, Biocaml_base.Gff.item, unit) t

val gff_unparser : [ `two | `three ] -> (Biocaml_base.Gff.item, string, unit) t

val table_parser : unit -> (string, string list, unit) t

val table_unparser : unit -> (string list, string, unit) t

val macs_xls_parser : (Biocaml_base.Line.t, Macs.Xls.item, unit) t

val macs_xls_unparser : (Macs.Xls.item, string, unit) t

val fasta_parser : unit -> (string, Biocaml_base.Fasta.item, unit) t