miga-base 0.3.8.0 → 0.3.8.1
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- checksums.yaml +4 -4
- data/actions/summary.rb +4 -4
- data/lib/miga/result/dates.rb +2 -1
- data/lib/miga/version.rb +1 -1
- data/utils/distance/commands.rb +5 -3
- data/utils/enveomics/Pipelines/assembly.pbs/FastA.N50.pl +1 -1
- data/utils/enveomics/Pipelines/assembly.pbs/FastA.filterN.pl +1 -1
- data/utils/enveomics/Pipelines/assembly.pbs/FastA.length.pl +1 -1
- data/utils/enveomics/Pipelines/blast.pbs/FastA.split.pl +1 -1
- data/utils/enveomics/Scripts/lib/enveomics.R +1 -1
- metadata +2 -3
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: bbf27a1aa7abe14e9b7fb0a32a3acaa82948f12034169dc1e065cbe05ec275f2
|
4
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+
data.tar.gz: 854b0793698f158b73ba2aab35638610db3e7044acf91a760fcd6ab272b81172
|
5
5
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SHA512:
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6
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-
metadata.gz:
|
7
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-
data.tar.gz:
|
6
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+
metadata.gz: f90b4de8827dc552cd570072714de6e7383ca38e6baa1603a9d730d28a83a247f327bc598937a84cf5bc9bd3fab888b9a42d39dd501e311b18abe0d934daa8b0
|
7
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+
data.tar.gz: 814bf34e30d1fde7e9f91403df099c61eecf6c0a7c4bf524e9cf70c0acd4c1b5052bc8168015c9883a35ed64f3ea813be033bc75ae0711094835597c3a9bafd7
|
data/actions/summary.rb
CHANGED
@@ -3,7 +3,7 @@
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3
3
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# @package MiGA
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4
4
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# @license Artistic-2.0
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5
5
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6
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-
o = {q:true, units:false, tabular:false}
|
6
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+
o = {q: true, units: false, tabular: false}
|
7
7
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opts = OptionParser.new do |opt|
|
8
8
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opt_banner(opt)
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9
9
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opt_object(opt, o, [:project, :dataset_opt])
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@@ -12,7 +12,7 @@ opts = OptionParser.new do |opt|
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12
12
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opt.on("--tab",
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13
13
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"Returns a tab-delimited table."){ |v| o[:tabular] = v }
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14
14
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opt.on("--key STRING",
|
15
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-
"Returns only the value of the requested key."){ |v| o[:
|
15
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+
"Returns only the value of the requested key."){ |v| o[:key_md] = v }
|
16
16
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opt.on("--with-units",
|
17
17
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"Includes units in each cell."){ |v| o[:units] = v }
|
18
18
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opt_common(opt, o)
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@@ -42,8 +42,8 @@ stats = ds.map do |d|
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|
42
42
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s = r.nil? ? {} : r[:stats]
|
43
43
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s.tap{ |i| i[:dataset] = d.name }
|
44
44
|
end
|
45
|
-
keys = o[:
|
46
|
-
[:dataset, o[:
|
45
|
+
keys = o[:key_md].nil? ? stats.map(&:keys).flatten.uniq :
|
46
|
+
[:dataset, o[:key_md].downcase.miga_name.to_sym]
|
47
47
|
keys.delete :dataset
|
48
48
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keys.unshift :dataset
|
49
49
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|
data/lib/miga/result/dates.rb
CHANGED
@@ -25,7 +25,7 @@ module MiGA::Result::Dates
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|
25
25
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def running_time
|
26
26
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a = started_at or return nil
|
27
27
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b = done_at or return nil
|
28
|
-
(b - a).to_f
|
28
|
+
(b - a).to_f / 60.0
|
29
29
|
end
|
30
30
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|
31
31
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private
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@@ -34,6 +34,7 @@ module MiGA::Result::Dates
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|
34
34
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# Internal function to detect start and end dates
|
35
35
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def date_at(event)
|
36
36
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date = self[event]
|
37
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+
date ||= self[:started] if event == :start
|
37
38
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if date.nil?
|
38
39
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f = path event
|
39
40
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date = File.read(f) if File.size? f
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data/lib/miga/version.rb
CHANGED
@@ -10,7 +10,7 @@ module MiGA
|
|
10
10
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# - Float representing the major.minor version.
|
11
11
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# - Integer representing gem releases of the current version.
|
12
12
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# - Integer representing minor changes that require new version number.
|
13
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-
VERSION = [0.3, 8,
|
13
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+
VERSION = [0.3, 8, 1]
|
14
14
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|
15
15
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##
|
16
16
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# Nickname for the current major.minor version.
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data/utils/distance/commands.rb
CHANGED
@@ -80,9 +80,11 @@ module MiGA::DistanceRunner::Commands
|
|
80
80
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if o[:ani_p] == 'fastani'
|
81
81
|
out = `fastANI -r "#{f1}" -q "#{f2}" \
|
82
82
|
-o /dev/stdout 2>/dev/null`.chomp.split(/\s+/)
|
83
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-
|
84
|
-
|
85
|
-
|
83
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+
unless out.empty?
|
84
|
+
SQLite3::Database.new(db) do |conn|
|
85
|
+
conn.execute "insert into ani values(?, ?, ?, 0, ?, ?)",
|
86
|
+
[n1, n2, out[2], out[3], out[4]]
|
87
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+
end
|
86
88
|
end
|
87
89
|
v = out[2]
|
88
90
|
else
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@@ -1 +1 @@
|
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1
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-
|
1
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+
../../Scripts/FastA.N50.pl
|
@@ -1 +1 @@
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1
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-
|
1
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+
../../Scripts/FastA.filterN.pl
|
@@ -1 +1 @@
|
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1
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-
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1
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+
../../Scripts/FastA.length.pl
|
@@ -1 +1 @@
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1
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-
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1
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+
../../Scripts/FastA.split.pl
|
@@ -1 +1 @@
|
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1
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-
|
1
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+
../../enveomics.R
|
metadata
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
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--- !ruby/object:Gem::Specification
|
2
2
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name: miga-base
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 0.3.8.
|
4
|
+
version: 0.3.8.1
|
5
5
|
platform: ruby
|
6
6
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authors:
|
7
7
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- Luis M. Rodriguez-R
|
@@ -496,8 +496,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
|
|
496
496
|
- !ruby/object:Gem::Version
|
497
497
|
version: '0'
|
498
498
|
requirements: []
|
499
|
-
|
500
|
-
rubygems_version: 2.7.7
|
499
|
+
rubygems_version: 3.0.2
|
501
500
|
signing_key:
|
502
501
|
specification_version: 4
|
503
502
|
summary: MiGA
|