miga-base 1.3.15.0 → 1.3.15.1
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +4 -4
- data/lib/miga/dataset/result/add.rb +3 -1
- data/lib/miga/version.rb +2 -2
- data/scripts/distances.bash +38 -36
- data/utils/distance/runner.rb +9 -1
- metadata +2 -2
checksums.yaml
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---
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SHA256:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 0b28d0e279592c817bf22a7ada5e292cfae35fff6d64b170499a9b8a9e662e89
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data.tar.gz: 5653a537b9468d7d4ec9a7a02712be6c3a4481d020909b757cc443ddab50f097
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 9f28050603a5e0a015b284cb09e88621a2650ef0eb6580b9ca6edf362dfd2ae19a50848e476ad9a7f66d4aa8c3a28ed51cdfef1f0566de72d3ba3b6f16596ce6
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data.tar.gz: 9e0aa59955542a9ac42f009965cc6e66e9fb7d55269298e554652b20afaca312454d1fbff09a08cd2660e9f2cbf33e10f120117ed5f5ddf853d871a4817f2de0
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@@ -261,10 +261,12 @@ module MiGA::Dataset::Result::Add
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def add_result_distances_nonref(base)
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return nil unless
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result_files_exist?(base, %w[.aai-medoids.tsv .aai.db]) ||
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result_files_exist?(base, %w[.ani-medoids.tsv .ani.db])
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result_files_exist?(base, %w[.ani-medoids.tsv .ani.db]) ||
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result_files_exist?(base, %w[.empty])
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add_files_to_ds_result(
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MiGA::Result.new("#{base}.json"), name,
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empty: '.empty',
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aai_medoids: '.aai-medoids.tsv',
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haai_db: '.haai.db',
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aai_db: '.aai.db',
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data/lib/miga/version.rb
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@@ -12,7 +12,7 @@ module MiGA
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# - String indicating release status:
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# - rc* release candidate, not released as gem
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# - [0-9]+ stable release, released as gem
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VERSION = [1.3, 15,
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VERSION = [1.3, 15, 1].freeze
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##
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# Nickname for the current major.minor version.
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##
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# Date of the current gem relese.
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VERSION_DATE = Date.new(2024, 5,
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VERSION_DATE = Date.new(2024, 5, 6)
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##
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# References of MiGA
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data/scripts/distances.bash
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blat=no
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diamond=no
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fastani=no
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fastaai
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diamond
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blast
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if [[ ! -s "${DATASET}.empty" ]] ; then
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case $(miga option -P "$PROJECT" -k haai_p) in
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fastaai)
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fastaai=yes
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;;
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diamond)
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diamond=yes
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aai=yes
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;;
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blast)
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blast=yes
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aai=yes
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;;
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esac
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case $(miga option -P "$PROJECT" -k aai_p) in
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esac
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case $(miga option -P "$PROJECT" -k aai_p) in
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diamond)
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diamond=yes
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aai=yes
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;;
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blast)
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blast=yes
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aai=yes
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;;
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esac
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case $(miga option -P "$PROJECT" -k ani_p) in
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esac
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case $(miga option -P "$PROJECT" -k ani_p) in
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blast)
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blast=yes
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ani=yes
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;;
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blat)
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blat=yes
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ani=yes
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;;
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fastani)
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fastani=yes
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;;
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esac
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fi
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miga date > "${DATASET}.done"
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data/utils/distance/runner.rb
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# Launch the appropriate analysis
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def go!
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$stderr.puts
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$stderr.puts 'Launching analysis'
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return if dataset.multi?
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Dir.mktmpdir do |tmp_dir|
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# Launch analysis for query datasets
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def go_query!
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$stderr.puts 'Launching analysis for query dataset'
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# Check if the project is empty
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if ref_project.dataset_ref_active.empty?
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out_base = File.expand_path(dataset.name, home)
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File.open("#{out_base}.empty", 'w') { |fh| fh.puts 'Empty ref_project' }
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return
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end
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# Check if project is ready
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tsk = ref_project.clade? ? [:subclades, :ani] : [:clade_finding, :aai]
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res = ref_project.result(tsk[0])
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metadata
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--- !ruby/object:Gem::Specification
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name: miga-base
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version: !ruby/object:Gem::Version
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version: 1.3.15.
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version: 1.3.15.1
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platform: ruby
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authors:
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- Luis M. Rodriguez-R
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autorequire:
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bindir: bin
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cert_chain: []
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date: 2024-05-
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date: 2024-05-06 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: daemons
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