bistro-bio 0.6.0 · 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

type chromosome_sequences = [ `ucsc_chromosome_sequences ] Bistro.directory

Dealing with genome sequences

val chromosome_sequence : [< genome ] -> string -> Formats.fasta Bistro.file

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

val genome_sequence : [< genome ] -> Formats.fasta Bistro.file

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

val twoBitToFa : 
  twobit Bistro.file ->
  Formats.bed4 Bistro.file ->
  Formats.fasta Bistro.file

val faToTwoBit : Formats.fasta Bistro.file -> twobit Bistro.file

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

Chromosome size and clipping

val bedClip : 
  chrom_sizes Bistro.file ->
  Formats.bed3 as 'a Bistro.file ->
  'a Bistro.file

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

Conversion between annotation file formats

val bedToBigBed : 
  [< genome ] ->
  [ `bed3 of Formats.bed3 Bistro.file | `bed5 of Formats.bed5 Bistro.file ] ->
  bigBed Bistro.file

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 Formats.bed3 Bistro.file | `bed5 of Formats.bed5 Bistro.file ] ->
  bigBed Bistro.file

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

module Lift_over : sig ... end

package bistro-bio