miga-base 1.2.13.1 → 1.2.13.2
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- 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
@@ -1,7 +1,7 @@
|
|
1
1
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---
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2
2
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SHA256:
|
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: 4251d1682329f32db78c304d4e35362930f004d07eedce3b176908d6d86f0bf0
|
4
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+
data.tar.gz: dc3612cbdb962003ec0804b0bc556f30511a69f1a4d945f8b4fb41a7f1c99799
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5
5
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SHA512:
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6
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-
metadata.gz:
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7
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-
data.tar.gz:
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6
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+
metadata.gz: 969b506228f5757a0ff276bf39df6f3ba2c0eaf0549b60e672c239733cafc92db461c4d622d986e70e5b986c8200625946b3fcbcdebcbfe7a089021865788b60
|
7
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+
data.tar.gz: 1851f909d65d61f724288830bd4475ce65d9fd16194dd9be1200d7723010cd1fc25f059a9c7c5ebbe6be2e74f2a52a39996aaa13e01d7e32cedf2a23bd228e11
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data/lib/miga/result/stats.rb
CHANGED
@@ -164,18 +164,24 @@ module MiGA::Result::Stats
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|
164
164
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lsu: 0, complete_lsu: 0, lsu_fragment: [0.0, '%']
|
165
165
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}
|
166
166
|
|
167
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+
subunits = {
|
168
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+
'16S_rRNA' => :ssu, '23S_rRNA' => :lsu,
|
169
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+
'18S_rRNA' => :ssu, '28S_rRNA' => :lsu
|
170
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+
}
|
167
171
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Zlib::GzipReader.open(file_path(:gff)) do |fh|
|
168
172
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fh.each_line do |ln|
|
169
173
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next if ln =~ /^#/
|
170
174
|
|
171
175
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rl = ln.chomp.split("\t")
|
172
176
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feat = Hash[rl[8].split(';').map { |i| i.split('=', 2) }]
|
173
|
-
subunit = feat['Name']
|
177
|
+
subunit = subunits[feat['Name']] or next # Ignore 5S
|
178
|
+
|
174
179
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if subunit == :ssu
|
175
180
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len = (rl[4].to_i - rl[3].to_i).abs + 1
|
176
181
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stats[:max_length] = [stats[:max_length] || 0, len].max
|
177
182
|
end
|
178
|
-
|
183
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+
|
184
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+
stats[subunit] += 1
|
179
185
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if feat['product'] =~ /\(partial\)/
|
180
186
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if feat['note'] =~ /aligned only (\d+) percent/
|
181
187
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fragment = $1.to_f
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@@ -185,7 +191,7 @@ module MiGA::Result::Stats
|
|
185
191
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end
|
186
192
|
else
|
187
193
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stats[:"complete_#{subunit}"] += 1
|
188
|
-
stats[:"#{subunit}_fragment"] =
|
194
|
+
stats[:"#{subunit}_fragment"][0] = 100.0
|
189
195
|
end
|
190
196
|
end
|
191
197
|
end
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data/lib/miga/version.rb
CHANGED
@@ -12,7 +12,7 @@ module MiGA
|
|
12
12
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# - String indicating release status:
|
13
13
|
# - rc* release candidate, not released as gem
|
14
14
|
# - [0-9]+ stable release, released as gem
|
15
|
-
VERSION = [1.2, 13,
|
15
|
+
VERSION = [1.2, 13, 2].freeze
|
16
16
|
|
17
17
|
##
|
18
18
|
# Nickname for the current major.minor version.
|