miga-base 1.2.1.0 → 1.2.2.0
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/version.rb +1 -1
- data/utils/distance/commands.rb +6 -1
- data/utils/distance/pipeline.rb +4 -0
- metadata +1 -1
checksums.yaml
CHANGED
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@@ -1,7 +1,7 @@
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1
1
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---
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2
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SHA256:
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3
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metadata.gz:
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4
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data.tar.gz:
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3
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metadata.gz: ab62d2e6d20aa126a5f455bd3b8159549d5c39b7b2e747587a0b0444a30d935a
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4
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data.tar.gz: 273671304affb6a21d1e4dc0374c4ff17edf39a96cba8893d2a666640ab1c7c9
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SHA512:
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metadata.gz:
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data.tar.gz:
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6
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metadata.gz: a157f0c4c52cfe4729eb5bda27900150153606b80f816a169ef18d6603b3fcd0ac03574cdbafbfcfe73e56a55ffbbf168a8c4316f066674ff6aebf6cef168500
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7
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data.tar.gz: 1a7b42d7dc75c5cac04f3408e6fba0e989d46ac63e926602c020e15340e24e8dc4694bf07b5f75ecc3a707db9d110d4a379841c426f7eb4a5670da5bcfa9642e
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data/lib/miga/version.rb
CHANGED
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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 = [1.2,
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VERSION = [1.2, 2, 0].freeze
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##
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# Nickname for the current major.minor version.
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data/utils/distance/commands.rb
CHANGED
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@@ -111,12 +111,17 @@ module MiGA::DistanceRunner::Commands
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return unless File.size?(f1)
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# Run FastANI
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empty = true
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File.open(f2 = tmp_file, 'w') do |fh|
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targets.each do |target|
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target_asm = target&.result(:assembly)&.file_path(:largecontigs)
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-
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if target_asm
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fh.puts target_asm
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empty = false
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end
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end
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end
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return if empty
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run_cmd <<~CMD
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fastANI -q "#{f1}" --rl "#{f2}" -t #{opts[:thr]} \
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-o "#{f3 = tmp_file}"
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data/utils/distance/pipeline.rb
CHANGED
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@@ -33,6 +33,10 @@ module MiGA::DistanceRunner::Pipeline
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# Builds a tree with all visited medoids from any classification level
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def build_medoids_tree(metric)
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# TODO Reduce impact and bring back the medoids tree
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$stderr.puts 'Bypassing medoids tree'
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return
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$stderr.puts "Building medoids tree (metric = #{metric})"
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db = query_db(metric)
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return unless File.size? db
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