Ucsc_gb (p.bistro.0.5.0.doc.bistro.bioinfo.Bistro_bioinfo.Ucsc

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

class type chromosome_sequences = object ... end

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

val chromosome_sequences : [< genome ] -> chromosome_sequences Bistro.pworkflow

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

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

val twoBitToFa : 
  twobit Bistro.pworkflow ->
  bed4 Bistro.pworkflow ->
  fasta Bistro.pworkflow

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

Chromosome size and clipping

val bedClip : 
  chrom_sizes Bistro.pworkflow ->
  (bed3 as 'a) Bistro.pworkflow ->
  'a Bistro.pworkflow

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

Conversion between annotation file formats

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

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 bed3 Bistro.pworkflow | `bed5 of bed5 Bistro.pworkflow ] ->
  bigBed Bistro.pworkflow

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

module Lift_over : sig ... end