package bistro-bio

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package bistro-bio
Legend:
Library
Module
Module type
Parameter
Class
Class type
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 = [
  1. | `dm3
  2. | `droSim1
  3. | `hg18
  4. | `hg19
  5. | `hg38
  6. | `mm8
  7. | `mm9
  8. | `mm10
  9. | `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 fetchChromSizes : [< genome ] -> chrom_sizes Bistro.file

Chromosome size and clipping

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