Class: MiGA::Project
Overview
MiGA representation of a project.
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/01.checkm 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 10.clades 10.clades/01.find 10.clades/02.ani 10.clades/03.ogs 10.clades/04.phylogeny 10.clades/04.phylogeny/01.essential 10.clades/04.phylogeny/02.core 10.clades/05.metadata ]
- @@RESULT_DIRS =
{ # 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 =
{ 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 =
[:haai_distances, :aai_distances, :ani_distances, :clade_finding]
- @@INCLADE_TASKS =
[:subclades, :ogs, :ess_phylogeny, :core_phylogeny, :clade_metadata]
Constants included from MiGA
CITATION, VERSION, VERSION_DATE, VERSION_NAME
Instance Attribute Summary collapse
-
#metadata ⇒ Object
readonly
Information about the project as MiGA::Metadata.
-
#path ⇒ Object
readonly
Absolute path to the project folder.
Class Method Summary collapse
-
.DISTANCE_TASKS ⇒ Object
Project-wide distance estimations.
-
.exist?(path) ⇒ Boolean
Does the project at
path
exist?. -
.INCLADE_TASKS ⇒ Object
Project-wide tasks for :clade projects.
-
.KNOWN_TYPES ⇒ Object
Supported types of projects.
-
.load(path) ⇒ Object
Load the project at
path
. -
.RESULT_DIRS ⇒ Object
Directories containing the results from project-wide tasks.
Instance Method Summary collapse
-
#add_dataset(name) ⇒ Object
Add dataset identified by
name
and return MiGA::Dataset. -
#add_result(name, save = true) ⇒ Object
Add the result identified by Symbol
name
, and return MiGA::Result. -
#create ⇒ Object
Create an empty project.
-
#dataset(name) ⇒ Object
Returns MiGA::Dataset.
-
#datasets ⇒ Object
Returns Array of MiGA::Dataset.
-
#done_preprocessing?(save = true) ⇒ Boolean
Are all the datasets in the project preprocessed? Save intermediate results if
save
. -
#each_dataset(&blk) ⇒ Object
Iterate through datasets, with a single variable MiGA::Dataset passed to
blk
. -
#each_dataset_profile_advance(&blk) ⇒ Object
Call
blk
passing the result of MiGA::Dataset#profile_advance for each registered dataset. -
#import_dataset(ds, method = :hardlink) ⇒ Object
Import the dataset
ds
, a MiGA::Dataset, usingmethod
which is any method supported by File#generic_transfer. -
#initialize(path, update = false) ⇒ Project
constructor
Create a new MiGA::Project at
path
, if it doesn’t exist andupdate
is false, or load an existing one. -
#load ⇒ Object
(Re-)load project data and metadata.
-
#name ⇒ Object
Name of the project.
-
#next_distances(save = true) ⇒ Object
Get the next distances task, saving intermediate results if
save
. -
#next_inclade(save = true) ⇒ Object
Get the next inclade task, saving intermediate results if
save
. -
#profile_datasets_advance ⇒ Object
Returns a two-dimensional matrix (Array of Array) where the first index corresponds to the dataset, the second index corresponds to the dataset task, and the value corresponds to: - 0: Before execution.
-
#result(name) ⇒ Object
Get result identified by Symbol
name
, returns MiGA::Result. -
#results ⇒ Object
Get all results, an Array of MiGA::Result.
-
#save ⇒ Object
Save any changes persistently.
-
#unlink_dataset(name) ⇒ Object
Unlink dataset identified by
name
and return MiGA::Dataset. -
#unregistered_datasets ⇒ Object
Find all datasets with (potential) result files but are yet unregistered.
Methods inherited from MiGA
CITATION, DEBUG, DEBUG_OFF, DEBUG_ON, DEBUG_TRACE_OFF, DEBUG_TRACE_ON, FULL_VERSION, LONG_VERSION, VERSION, VERSION_DATE, initialized?, #result_files_exist?, root_path, tabulate
Constructor Details
#initialize(path, update = false) ⇒ Project
Create a new MiGA::Project at path
, if it doesn’t exist and update
is false, or load an existing one.
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# File 'lib/miga/project.rb', line 108 def initialize(path, update=false) @datasets = {} @path = File.absolute_path(path) self.create if update or not Project.exist? self.path self.load if self..nil? end |
Instance Attribute Details
#metadata ⇒ Object (readonly)
Information about the project as MiGA::Metadata.
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# File 'lib/miga/project.rb', line 103 def @metadata end |
#path ⇒ Object (readonly)
Absolute path to the project folder.
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# File 'lib/miga/project.rb', line 99 def path @path end |
Class Method Details
.DISTANCE_TASKS ⇒ Object
Project-wide distance estimations.
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# File 'lib/miga/project.rb', line 71 def self.DISTANCE_TASKS ; @@DISTANCE_TASKS ; end |
.exist?(path) ⇒ Boolean
Does the project at path
exist?
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# File 'lib/miga/project.rb', line 83 def self.exist?(path) Dir.exist?(path) and File.exist?(path + "/miga.project.json") end |
.INCLADE_TASKS ⇒ Object
Project-wide tasks for :clade projects.
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# File 'lib/miga/project.rb', line 77 def self.INCLADE_TASKS ; @@INCLADE_TASKS ; end |
.KNOWN_TYPES ⇒ Object
Supported types of projects.
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# File 'lib/miga/project.rb', line 56 def self.KNOWN_TYPES ; @@KNOWN_TYPES ; end |
.load(path) ⇒ Object
Load the project at path
. Returns MiGA::Project if project exists, nil otherwise.
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# File 'lib/miga/project.rb', line 90 def self.load(path) return nil unless Project.exist? path Project.new path end |
.RESULT_DIRS ⇒ Object
Directories containing the results from project-wide tasks.
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# File 'lib/miga/project.rb', line 37 def self.RESULT_DIRS ; @@RESULT_DIRS ; end |
Instance Method Details
#add_dataset(name) ⇒ Object
Add dataset identified by name
and return MiGA::Dataset.
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# File 'lib/miga/project.rb', line 175 def add_dataset(name) unless [:datasets].include? name d = MiGA::Dataset.new(self, name) @metadata[:datasets] << name save end dataset(name) end |
#add_result(name, save = true) ⇒ Object
Add the result identified by Symbol name
, and return MiGA::Result. Save the result if save
.
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# File 'lib/miga/project.rb', line 240 def add_result(name, save=true) return nil if @@RESULT_DIRS[name].nil? base = "#{path}/data/#{@@RESULT_DIRS[name]}/miga-project" return MiGA::Result.load(base + ".json") unless save return nil unless result_files_exist?(base, ".done") r = send("add_result_#{name}", base) r.save r end |
#create ⇒ Object
Create an empty project.
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# File 'lib/miga/project.rb', line 117 def create unless MiGA::MiGA.initialized? raise "Impossible to create project in uninitialized MiGA." end dirs = [path] + @@FOLDERS.map{|d| "#{path}/#{d}" } + @@DATA_FOLDERS.map{ |d| "#{path}/data/#{d}"} dirs.each{ |d| Dir.mkdir(d) unless Dir.exist? d } @metadata = MiGA::Metadata.new(self.path + "/miga.project.json", {datasets: [], name: File.basename(path)}) FileUtils.cp(ENV["MIGA_HOME"] + "/.miga_daemon.json", "#{path}/daemon/daemon.json") unless File.exist? "#{path}/daemon/daemon.json" self.load end |
#dataset(name) ⇒ Object
Returns MiGA::Dataset.
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# File 'lib/miga/project.rb', line 158 def dataset(name) name = name.miga_name return nil unless MiGA::Dataset.exist?(self, name) @datasets ||= {} @datasets[name] ||= MiGA::Dataset.new(self, name) @datasets[name] end |
#datasets ⇒ Object
Returns Array of MiGA::Dataset.
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# File 'lib/miga/project.rb', line 152 def datasets [:datasets].map{ |name| dataset(name) } end |
#done_preprocessing?(save = true) ⇒ Boolean
Are all the datasets in the project preprocessed? Save intermediate results if save
.
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# File 'lib/miga/project.rb', line 285 def done_preprocessing?(save=true) datasets.map{|ds| (not ds.is_ref?) or ds.done_preprocessing?(save) }.all? end |
#each_dataset(&blk) ⇒ Object
Iterate through datasets, with a single variable MiGA::Dataset passed to blk
.
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# File 'lib/miga/project.rb', line 169 def each_dataset(&blk) [:datasets].each{ |name| blk.call(dataset(name)) } end |
#each_dataset_profile_advance(&blk) ⇒ Object
Call blk
passing the result of MiGA::Dataset#profile_advance for each registered dataset.
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# File 'lib/miga/project.rb', line 307 def each_dataset_profile_advance(&blk) each_dataset { |ds| blk.call(ds.profile_advance) } end |
#import_dataset(ds, method = :hardlink) ⇒ Object
Import the dataset ds
, a MiGA::Dataset, using method
which is any method supported by File#generic_transfer.
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# File 'lib/miga/project.rb', line 197 def import_dataset(ds, method=:hardlink) raise "Impossible to import dataset, it already exists: #{ds.name}." if MiGA::Dataset.exist?(self, ds.name) # Import dataset results ds.each_result do |task, result| # import result files result.each_file do |file| File.generic_transfer("#{result.dir}/#{file}", "#{path}/data/#{MiGA::Dataset.RESULT_DIRS[task]}/#{file}", method) end # import result metadata %w(json start done).each do |suffix| if File.exist? "#{result.dir}/#{ds.name}.#{suffix}" File.generic_transfer("#{result.dir}/#{ds.name}.#{suffix}", "#{path}/data/#{MiGA::Dataset.RESULT_DIRS[task]}/" + "#{ds.name}.#{suffix}", method) end end end # Import dataset metadata File.generic_transfer("#{ds.project.path}/metadata/#{ds.name}.json", "#{self.path}/metadata/#{ds.name}.json", method) # Save dataset self.add_dataset(ds.name) end |
#load ⇒ Object
(Re-)load project data and metadata.
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# File 'lib/miga/project.rb', line 141 def load @metadata = MiGA::Metadata.load "#{path}/miga.project.json" raise "Couldn't find project metadata at #{path}" if .nil? end |
#name ⇒ Object
Name of the project.
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# File 'lib/miga/project.rb', line 148 def name ; [:name] ; end |
#next_distances(save = true) ⇒ Object
Get the next distances task, saving intermediate results if save
. Returns a Symbol.
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# File 'lib/miga/project.rb', line 253 def next_distances(save=true) @@DISTANCE_TASKS.find{ |t| add_result(t, save).nil? } end |
#next_inclade(save = true) ⇒ Object
Get the next inclade task, saving intermediate results if save
. Returns a Symbol.
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# File 'lib/miga/project.rb', line 260 def next_inclade(save=true) return nil unless [:type]==:clade @@INCLADE_TASKS.find{ |t| add_result(t, save).nil? } end |
#profile_datasets_advance ⇒ Object
Returns a two-dimensional matrix (Array of Array) where the first index corresponds to the dataset, the second index corresponds to the dataset task, and the value corresponds to:
-
0: Before execution.
-
1: Done (or not required).
-
2: To do.
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# File 'lib/miga/project.rb', line 296 def profile_datasets_advance advance = [] self.each_dataset_profile_advance do |ds_adv| advance << ds_adv end advance end |
#result(name) ⇒ Object
Get result identified by Symbol name
, returns MiGA::Result.
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# File 'lib/miga/project.rb', line 225 def result(name) return nil if @@RESULT_DIRS[name.to_sym].nil? MiGA::Result.load "#{path}/data/" + @@RESULT_DIRS[name.to_sym] + "/miga-project.json" end |
#results ⇒ Object
Get all results, an Array of MiGA::Result.
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# File 'lib/miga/project.rb', line 233 def results @@RESULT_DIRS.keys.map{ |k| result(k) }.reject{ |r| r.nil? } end |
#save ⇒ Object
Save any changes persistently.
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# File 'lib/miga/project.rb', line 134 def save .save self.load end |
#unlink_dataset(name) ⇒ Object
Unlink dataset identified by name
and return MiGA::Dataset.
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# File 'lib/miga/project.rb', line 186 def unlink_dataset(name) d = dataset(name) return nil if d.nil? self.[:datasets].delete(name) save d end |
#unregistered_datasets ⇒ Object
Find all datasets with (potential) result files but are yet unregistered.
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# File 'lib/miga/project.rb', line 267 def unregistered_datasets datasets = [] MiGA::Dataset.RESULT_DIRS.values.each do |dir| Dir.entries("#{path}/data/#{dir}").each do |file| next unless file =~ %r{ \.(fa(a|sta|stqc?)?|fna|solexaqa|gff[23]?|done|ess)(\.gz)?$ }x m = /([^\.]+)/.match(file) datasets << m[1] unless m.nil? or m[1] == "miga-project" end end datasets.uniq - [:datasets] end |