Module Bistro_bioinfo.Ucsc_gb

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 : Bistro_bioinfo.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 ‑> Bistro_bioinfo.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