bistro 0.4.0 · OCaml Package

class type twobit = object ... end

class type chrom_sizes = object ... end

class type bigBed = object ... end

class type bedGraph = object ... end

class type wig = object ... end

class type bigWig = object ... end

type genome = [

| `dm3
| `droSim1
| `hg18
| `hg19
| `hg38
| `mm8
| `mm9
| `mm10
| `sacCer2

]

val string_of_genome : [< genome ] -> string

val genome_of_string : string -> genome option

val chromosome_sequence : 
  [< genome ] ->
  string ->
  Defs.fasta Bistro.Std.workflow

Dealing with genome sequences

val chromosome_sequences : 
  [< genome ] ->
  [ `ucsc_chromosome_sequences ] Bistro.Std.directory Bistro.Std.workflow

val genome_sequence : [< genome ] -> Defs.fasta Bistro.Std.workflow

val genome_2bit_sequence : [< genome ] -> twobit Bistro.Std.workflow

val twoBitToFa : 
  Defs.bed4 Bistro.Std.workflow ->
  twobit Bistro.Std.workflow ->
  Defs.fasta Bistro.Std.workflow

val fetchChromSizes : [< genome ] -> chrom_sizes Bistro.Std.workflow

Chromosome size and clipping

val bedClip : 
  chrom_sizes Bistro.Std.workflow ->
  Defs.bed3 as 'a Bistro.Std.workflow ->
  'a Bistro.Std.workflow

val bedGraphToBigWig : 
  [< genome ] ->
  bedGraph Bistro.Std.workflow ->
  bigWig Bistro.Std.workflow

Conversion between annotation file formats

val bedToBigBed : 
  [< genome ] ->
  [ `bed3 of Defs.bed3 Bistro.Std.workflow
  | `bed5 of Defs.bed5 Bistro.Std.workflow ] ->
  bigBed Bistro.Std.workflow

bedToBigBed

utility. Fails when given an empty BED file on input. Note that the underlying

bedToBigBed

expects BED files with exactly 3 or 5 columns.

val bedToBigBed_failsafe : 
  [< genome ] ->
  [ `bed3 of Defs.bed3 Bistro.Std.workflow
  | `bed5 of Defs.bed5 Bistro.Std.workflow ] ->
  bigBed Bistro.Std.workflow

sam as Ucsc_gb.bedToBigBed but produces an empty file when given an empty BED on input.

module Lift_over : sig ... end