miga-base 1.2.13.1 → 1.2.13.2
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/result/stats.rb +9 -3
- data/lib/miga/version.rb +1 -1
- metadata +1 -1
checksums.yaml
CHANGED
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@@ -1,7 +1,7 @@
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1
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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: 4251d1682329f32db78c304d4e35362930f004d07eedce3b176908d6d86f0bf0
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4
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data.tar.gz: dc3612cbdb962003ec0804b0bc556f30511a69f1a4d945f8b4fb41a7f1c99799
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 969b506228f5757a0ff276bf39df6f3ba2c0eaf0549b60e672c239733cafc92db461c4d622d986e70e5b986c8200625946b3fcbcdebcbfe7a089021865788b60
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7
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data.tar.gz: 1851f909d65d61f724288830bd4475ce65d9fd16194dd9be1200d7723010cd1fc25f059a9c7c5ebbe6be2e74f2a52a39996aaa13e01d7e32cedf2a23bd228e11
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data/lib/miga/result/stats.rb
CHANGED
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@@ -164,18 +164,24 @@ module MiGA::Result::Stats
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lsu: 0, complete_lsu: 0, lsu_fragment: [0.0, '%']
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}
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subunits = {
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'16S_rRNA' => :ssu, '23S_rRNA' => :lsu,
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'18S_rRNA' => :ssu, '28S_rRNA' => :lsu
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}
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Zlib::GzipReader.open(file_path(:gff)) do |fh|
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fh.each_line do |ln|
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next if ln =~ /^#/
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rl = ln.chomp.split("\t")
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feat = Hash[rl[8].split(';').map { |i| i.split('=', 2) }]
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-
subunit = feat['Name']
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subunit = subunits[feat['Name']] or next # Ignore 5S
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if subunit == :ssu
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len = (rl[4].to_i - rl[3].to_i).abs + 1
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stats[:max_length] = [stats[:max_length] || 0, len].max
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end
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-
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+
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stats[subunit] += 1
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if feat['product'] =~ /\(partial\)/
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if feat['note'] =~ /aligned only (\d+) percent/
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fragment = $1.to_f
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@@ -185,7 +191,7 @@ module MiGA::Result::Stats
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end
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else
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stats[:"complete_#{subunit}"] += 1
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-
stats[:"#{subunit}_fragment"] =
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stats[:"#{subunit}_fragment"][0] = 100.0
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end
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end
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end
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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, 13,
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VERSION = [1.2, 13, 2].freeze
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##
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# Nickname for the current major.minor version.
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