Module: MiGA::Project::Base

Included in:: Result

Defined in:: lib/miga/project/base.rb

Constant Summary collapse

@@FOLDERS = Top-level folders inside a project

%w[data metadata daemon]

@@DATA_FOLDERS = Folders for results

%w[
  01.raw_reads 02.trimmed_reads 03.read_quality 04.trimmed_fasta
  05.assembly 06.cds
  07.annotation 07.annotation/01.function 07.annotation/02.taxonomy
  07.annotation/01.function/01.essential
  07.annotation/01.function/02.ssu
  07.annotation/02.taxonomy/01.mytaxa
  07.annotation/03.qa 07.annotation/03.qa/02.mytaxa_scan
  08.mapping 08.mapping/01.read-ctg 08.mapping/02.read-gene
  09.distances 09.distances/01.haai 09.distances/02.aai
  09.distances/03.ani 09.distances/04.ssu 09.distances/05.taxonomy
  10.clades 10.clades/01.find 10.clades/02.ani 10.clades/03.ogs
  90.stats
]

@@RESULT_DIRS = Directories containing the results from project-wide tasks

{
  project_stats: '90.stats',
  # Distances
  haai_distances: '09.distances/01.haai',
  aai_distances: '09.distances/02.aai',
  ani_distances: '09.distances/03.ani',
  # ssu_distances: '09.distances/04.ssu',
  # Clade identification
  clade_finding: '10.clades/01.find',
  # Clade analysis
  subclades: '10.clades/02.ani',
  ogs: '10.clades/03.ogs'
  # ess_phylogeny: '10.clades/04.phylogeny/01.essential',
  # core_phylogeny: '10.clades/04.phylogeny/02.core',
  # clade_metadata: '10.clades/05.metadata'
}

@@KNOWN_TYPES = Supported types of projects

{
  mixed: {
    description: 'Mixed collection of genomes, metagenomes, and viromes',
    single: true, multi: true
  },
  genomes: {
    description: 'Collection of genomes',
    single: true, multi: false
  },
  clade: {
    description: 'Collection of closely-related genomes (ANI >= 90%)',
    single: true, multi: false
  },
  metagenomes: {
    description: 'Collection of metagenomes and/or viromes',
    single: false, multi: true
  }
}

@@DISTANCE_TASKS = Project-wide distance estimations

[
  :project_stats, :haai_distances, :aai_distances, :ani_distances,
  :clade_finding
]

@@INCLADE_TASKS = Project-wide tasks for :clade projects

[:subclades, :ogs]

@@OPTIONS = Options supported by projects

{
  ref_project: {
    desc: 'Project with reference taxonomy', type: String
  },
  db_proj_dir: {
    desc: 'Directory containing database projects', type: String
  },
  tax_pvalue: {
    desc: 'Maximum p-value to transfer taxonomy', default: 0.05, type: Float,
    in: 0.0..1.0
  },
  haai_p: {
    desc: 'Value of aai.rb -p on hAAI', type: String,
    default: proc { |project| project.clade? ? 'no' : 'fastaai' },
    in: %w[blast+ blast blat diamond fastaai no]
  },
  aai_p: {
    desc: 'Value of aai.rb -p on AAI', default: 'diamond', type: String,
    in: %w[blast+ blast blat diamond]
  },
  ani_p: {
    desc: 'Value of ani.rb -p on ANI', default: 'fastani', type: String,
    in: %w[blast+ blast blat fastani]
  },
  max_try: {
    desc: 'Maximum number of task attempts', default: 10, type: Integer,
    in: (0..1000)
  },
  aai_save_rbm: {
    desc: 'Should RBMs be saved for OGS analysis?',
    default: proc { |project| project.clade? },
    in: [true, false]
  },
  ogs_identity: {
    desc: 'Min RBM identity for OGS', default: 80.0, type: Float,
    in: (0.0..100.0)
  },
  clean_ogs: {
    desc: 'If false, keeps ABC files (clades only)', default: true,
    in: [true, false]
  },
  run_clades: {
    desc: 'Should clades be estimated from distances?', default: true,
    in: [true, false]
  },
  gsp_ani: {
    desc: 'ANI limit to propose gsp clades', default: 95.0, type: Float,
    in: (0.0..100.0)
  },
  gsp_aai: {
    desc: 'AAI limit to propose gsp clades', default: 90.0, type: Float,
    in: (0.0..100.0)
  },
  gsp_metric: {
    desc: 'Metric to propose clades', default: 'ani', type: String,
    in: %w[ani aai]
  },
  ess_coll: {
    desc: 'Collection of essential genes to use', default: 'dupont_2012',
    type: String, in: %w[dupont_2012 lee_2019]
  },
  min_qual: {
    desc: 'Minimum genome quality', default: 25.0, type: Float,
    in: -Float::INFINITY..100.0, tokens: %w[no]
  },
  distances_checkpoint: {
    desc: 'Number of comparisons before storing data', default: 10,
    type: Integer, in: 1...Float::INFINITY
  }
}