miga-base 1.3.15.0 → 1.3.15.1
Sign up to get free protection for your applications and to get access to all the features.
- 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
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
|
---
|
2
2
|
SHA256:
|
3
|
-
metadata.gz:
|
4
|
-
data.tar.gz:
|
3
|
+
metadata.gz: 0b28d0e279592c817bf22a7ada5e292cfae35fff6d64b170499a9b8a9e662e89
|
4
|
+
data.tar.gz: 5653a537b9468d7d4ec9a7a02712be6c3a4481d020909b757cc443ddab50f097
|
5
5
|
SHA512:
|
6
|
-
metadata.gz:
|
7
|
-
data.tar.gz:
|
6
|
+
metadata.gz: 9f28050603a5e0a015b284cb09e88621a2650ef0eb6580b9ca6edf362dfd2ae19a50848e476ad9a7f66d4aa8c3a28ed51cdfef1f0566de72d3ba3b6f16596ce6
|
7
|
+
data.tar.gz: 9e0aa59955542a9ac42f009965cc6e66e9fb7d55269298e554652b20afaca312454d1fbff09a08cd2660e9f2cbf33e10f120117ed5f5ddf853d871a4817f2de0
|
@@ -261,10 +261,12 @@ module MiGA::Dataset::Result::Add
|
|
261
261
|
def add_result_distances_nonref(base)
|
262
262
|
return nil unless
|
263
263
|
result_files_exist?(base, %w[.aai-medoids.tsv .aai.db]) ||
|
264
|
-
result_files_exist?(base, %w[.ani-medoids.tsv .ani.db])
|
264
|
+
result_files_exist?(base, %w[.ani-medoids.tsv .ani.db]) ||
|
265
|
+
result_files_exist?(base, %w[.empty])
|
265
266
|
|
266
267
|
add_files_to_ds_result(
|
267
268
|
MiGA::Result.new("#{base}.json"), name,
|
269
|
+
empty: '.empty',
|
268
270
|
aai_medoids: '.aai-medoids.tsv',
|
269
271
|
haai_db: '.haai.db',
|
270
272
|
aai_db: '.aai.db',
|
data/lib/miga/version.rb
CHANGED
@@ -12,7 +12,7 @@ module MiGA
|
|
12
12
|
# - String indicating release status:
|
13
13
|
# - rc* release candidate, not released as gem
|
14
14
|
# - [0-9]+ stable release, released as gem
|
15
|
-
VERSION = [1.3, 15,
|
15
|
+
VERSION = [1.3, 15, 1].freeze
|
16
16
|
|
17
17
|
##
|
18
18
|
# Nickname for the current major.minor version.
|
@@ -20,7 +20,7 @@ module MiGA
|
|
20
20
|
|
21
21
|
##
|
22
22
|
# Date of the current gem relese.
|
23
|
-
VERSION_DATE = Date.new(2024, 5,
|
23
|
+
VERSION_DATE = Date.new(2024, 5, 6)
|
24
24
|
|
25
25
|
##
|
26
26
|
# References of MiGA
|
data/scripts/distances.bash
CHANGED
@@ -29,44 +29,46 @@ blast=no
|
|
29
29
|
blat=no
|
30
30
|
diamond=no
|
31
31
|
fastani=no
|
32
|
-
|
33
|
-
|
34
|
-
fastaai
|
35
|
-
|
36
|
-
|
37
|
-
diamond
|
38
|
-
|
39
|
-
|
40
|
-
|
41
|
-
blast
|
42
|
-
|
43
|
-
|
44
|
-
|
32
|
+
if [[ ! -s "${DATASET}.empty" ]] ; then
|
33
|
+
case $(miga option -P "$PROJECT" -k haai_p) in
|
34
|
+
fastaai)
|
35
|
+
fastaai=yes
|
36
|
+
;;
|
37
|
+
diamond)
|
38
|
+
diamond=yes
|
39
|
+
aai=yes
|
40
|
+
;;
|
41
|
+
blast)
|
42
|
+
blast=yes
|
43
|
+
aai=yes
|
44
|
+
;;
|
45
|
+
esac
|
45
46
|
|
46
|
-
case $(miga option -P "$PROJECT" -k aai_p) in
|
47
|
-
|
48
|
-
|
49
|
-
|
50
|
-
|
51
|
-
|
52
|
-
|
53
|
-
|
54
|
-
|
55
|
-
esac
|
47
|
+
case $(miga option -P "$PROJECT" -k aai_p) in
|
48
|
+
diamond)
|
49
|
+
diamond=yes
|
50
|
+
aai=yes
|
51
|
+
;;
|
52
|
+
blast)
|
53
|
+
blast=yes
|
54
|
+
aai=yes
|
55
|
+
;;
|
56
|
+
esac
|
56
57
|
|
57
|
-
case $(miga option -P "$PROJECT" -k ani_p) in
|
58
|
-
|
59
|
-
|
60
|
-
|
61
|
-
|
62
|
-
|
63
|
-
|
64
|
-
|
65
|
-
|
66
|
-
|
67
|
-
|
68
|
-
|
69
|
-
esac
|
58
|
+
case $(miga option -P "$PROJECT" -k ani_p) in
|
59
|
+
blast)
|
60
|
+
blast=yes
|
61
|
+
ani=yes
|
62
|
+
;;
|
63
|
+
blat)
|
64
|
+
blat=yes
|
65
|
+
ani=yes
|
66
|
+
;;
|
67
|
+
fastani)
|
68
|
+
fastani=yes
|
69
|
+
;;
|
70
|
+
esac
|
71
|
+
fi
|
70
72
|
|
71
73
|
|
72
74
|
miga date > "${DATASET}.done"
|
data/utils/distance/runner.rb
CHANGED
@@ -35,7 +35,7 @@ class MiGA::DistanceRunner
|
|
35
35
|
|
36
36
|
# Launch the appropriate analysis
|
37
37
|
def go!
|
38
|
-
$stderr.puts
|
38
|
+
$stderr.puts 'Launching analysis'
|
39
39
|
return if dataset.multi?
|
40
40
|
|
41
41
|
Dir.mktmpdir do |tmp_dir|
|
@@ -68,6 +68,14 @@ class MiGA::DistanceRunner
|
|
68
68
|
# Launch analysis for query datasets
|
69
69
|
def go_query!
|
70
70
|
$stderr.puts 'Launching analysis for query dataset'
|
71
|
+
|
72
|
+
# Check if the project is empty
|
73
|
+
if ref_project.dataset_ref_active.empty?
|
74
|
+
out_base = File.expand_path(dataset.name, home)
|
75
|
+
File.open("#{out_base}.empty", 'w') { |fh| fh.puts 'Empty ref_project' }
|
76
|
+
return
|
77
|
+
end
|
78
|
+
|
71
79
|
# Check if project is ready
|
72
80
|
tsk = ref_project.clade? ? [:subclades, :ani] : [:clade_finding, :aai]
|
73
81
|
res = ref_project.result(tsk[0])
|
metadata
CHANGED
@@ -1,14 +1,14 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: miga-base
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 1.3.15.
|
4
|
+
version: 1.3.15.1
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
7
|
- Luis M. Rodriguez-R
|
8
8
|
autorequire:
|
9
9
|
bindir: bin
|
10
10
|
cert_chain: []
|
11
|
-
date: 2024-05-
|
11
|
+
date: 2024-05-06 00:00:00.000000000 Z
|
12
12
|
dependencies:
|
13
13
|
- !ruby/object:Gem::Dependency
|
14
14
|
name: daemons
|