file_formats.ml 985 Bytes
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open Bistro.Std
open Bistro_bioinfo.Std

class type nhx = object
  inherit text_file
  method format : [`nhx]
end

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class type diffsel_tree = object
  inherit text_file
  method format : [`diffsel_tree]
end

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class type nucleotide_fasta = object
  inherit fasta
  method alphabet : [`Nucleotide]
end
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class type aminoacid_fasta = object
  inherit fasta
  method alphabet : [`Nucleotide]
end


type parsed_input_tree

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type output_parse_input_tree =
  | Nodes_H0
  | Nodes_Ha
  | Tree4detect
  | Tree4simu
  | Tree_diffsel
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type raw_dataset = {
  input_tree: nhx workflow ;
  fna: nucleotide_fasta workflow ;
  }

type ready_dataset = {
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  input_tree: nhx workflow ;
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  tree_dataset : [`tree_dataset] directory workflow ;
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  fna: nucleotide_fasta workflow ;
  faa: aminoacid_fasta workflow ;
  }
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type ('a,'b) w_dataset =
  | Raw_dataset of 'a
  | Ready_dataset of 'b


type dataset = {
  model_prefix: string ;
  tree_prefix : string ;
  dataset : (raw_dataset,ready_dataset) w_dataset
  }