package bistro-bio

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package bistro-bio
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Module Bistro_bio.Ucsc_gbSource

Sourceclass type twobit = object ... end
Sourceclass type chrom_sizes = object ... end
Sourceclass type bigBed = object ... end
Sourceclass type bedGraph = object ... end
Sourceclass type wig = object ... end
Sourceclass type bigWig = object ... end
Sourcetype genome = [
  1. | `dm3
  2. | `droSim1
  3. | `hg18
  4. | `hg19
  5. | `hg38
  6. | `mm8
  7. | `mm9
  8. | `mm10
  9. | `sacCer2
]
Sourceval string_of_genome : [< genome ] -> string
Sourceval genome_of_string : string -> genome option
Sourcetype chromosome_sequences = [ `ucsc_chromosome_sequences ] Bistro.directory

Dealing with genome sequences

Sourceval chromosome_sequence : [< genome ] -> string -> Formats.fasta Bistro.file
Sourceval chromosome_sequences : [< genome ] -> [ `ucsc_chromosome_sequences ] Bistro.directory
Sourceval genome_sequence : [< genome ] -> Formats.fasta Bistro.file
Sourceval genome_2bit_sequence : [< genome ] -> twobit Bistro.file
Sourceval twoBitToFa : twobit Bistro.file -> Formats.bed4 Bistro.file -> Formats.fasta Bistro.file
Sourceval faToTwoBit : Formats.fasta Bistro.file -> twobit Bistro.file
Sourceval fetchChromSizes : [< genome ] -> chrom_sizes Bistro.file

Chromosome size and clipping

Sourceval bedClip : chrom_sizes Bistro.file -> (Formats.bed3 as 'a) Bistro.file -> 'a Bistro.file
Sourceval bedGraphToBigWig : [< genome ] -> bedGraph Bistro.file -> bigWig Bistro.file

Conversion between annotation file formats

Sourceval 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.

Sourceval 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.

Sourcemodule Lift_over : sig ... end
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