miga-base 1.3.14.4 → 1.3.14.7
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 +2 -2
- data/scripts/aai_distances.bash +12 -5
- data/scripts/ani_distances.bash +12 -5
- data/test/remote_dataset_test.rb +1 -4
- 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: b637dd7bbd8ebd512621bf3781286c3f8f94f0ce916ade1d9913a08e93d31019
|
|
4
|
+
data.tar.gz: bca1c28c21031b4ceafba9192b2345124bed56278855829f255d2b0f9df0e933
|
|
5
5
|
SHA512:
|
|
6
|
-
metadata.gz:
|
|
7
|
-
data.tar.gz:
|
|
6
|
+
metadata.gz: '028b1b2c993a2b21528fb1d29a3b29d7a9f6333f6a8408e47773d84813341217d733cbdb4686a95264189df186ad884182b44ee2c2da86d3ccf696c02241971d'
|
|
7
|
+
data.tar.gz: 3e78e598542be5bfba5845e0ff8e4744d6413c5d0714be6bfef5e1202e02c9910fe569f1692b325dbaaef5697355cc9ee1eff90d0503730993ddf5bcf468a8e7
|
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, 14,
|
|
15
|
+
VERSION = [1.3, 14, 7].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, 4,
|
|
23
|
+
VERSION_DATE = Date.new(2024, 4, 24)
|
|
24
24
|
|
|
25
25
|
##
|
|
26
26
|
# References of MiGA
|
data/scripts/aai_distances.bash
CHANGED
|
@@ -40,11 +40,18 @@ rm "miga-project.txt.lno"
|
|
|
40
40
|
# R-ify
|
|
41
41
|
cat <<R | R --vanilla
|
|
42
42
|
file <- gzfile("miga-project.txt.gz")
|
|
43
|
-
text <- readLines(file, n = $LNO + 1, ok = FALSE)
|
|
44
|
-
|
|
45
|
-
|
|
46
|
-
|
|
47
|
-
|
|
43
|
+
text <- readLines(file, n = $LNO + 1, ok = FALSE)[-1]
|
|
44
|
+
a <- vector("character", $LNO)
|
|
45
|
+
b <- vector("character", $LNO)
|
|
46
|
+
d <- vector("numeric", $LNO)
|
|
47
|
+
chunk.n <- 1024 * 1024
|
|
48
|
+
for (chunk in seq_len(ceiling(length(text) / chunk.n))) {
|
|
49
|
+
sel <- (chunk * chunk.n - chunk.n + 1):min(chunk * chunk.n, length(text))
|
|
50
|
+
list <- strsplit(text[sel], "\t", fixed = TRUE)
|
|
51
|
+
a[sel] <- sapply(list, function(x) x[1])
|
|
52
|
+
b[sel] <- sapply(list, function(x) x[2])
|
|
53
|
+
d[sel] <- sapply(list, function(x) 1 - (as.numeric(x[3]) / 100))
|
|
54
|
+
}
|
|
48
55
|
save(a, b, d, file = "miga-project.rda")
|
|
49
56
|
|
|
50
57
|
non_self <- a != b
|
data/scripts/ani_distances.bash
CHANGED
|
@@ -34,11 +34,18 @@ rm "miga-project.txt.lno"
|
|
|
34
34
|
# R-ify
|
|
35
35
|
cat <<R | R --vanilla
|
|
36
36
|
file <- gzfile("miga-project.txt.gz")
|
|
37
|
-
text <- readLines(file, n = $LNO + 1, ok = FALSE)
|
|
38
|
-
|
|
39
|
-
|
|
40
|
-
|
|
41
|
-
|
|
37
|
+
text <- readLines(file, n = $LNO + 1, ok = FALSE)[-1]
|
|
38
|
+
a <- vector("character", $LNO)
|
|
39
|
+
b <- vector("character", $LNO)
|
|
40
|
+
d <- vector("numeric", $LNO)
|
|
41
|
+
chunk.n <- 1024 * 1024
|
|
42
|
+
for (chunk in seq_len(ceiling(length(text) / chunk.n))) {
|
|
43
|
+
sel <- (chunk * chunk.n - chunk.n + 1):min(chunk * chunk.n, length(text))
|
|
44
|
+
list <- strsplit(text[sel], "\t", fixed = TRUE)
|
|
45
|
+
a[sel] <- sapply(list, function(x) x[1])
|
|
46
|
+
b[sel] <- sapply(list, function(x) x[2])
|
|
47
|
+
d[sel] <- sapply(list, function(x) 1 - (as.numeric(x[3]) / 100))
|
|
48
|
+
}
|
|
42
49
|
save(a, b, d, file = "miga-project.rda")
|
|
43
50
|
|
|
44
51
|
non_self <- a != b
|
data/test/remote_dataset_test.rb
CHANGED
|
@@ -22,10 +22,7 @@ class RemoteDatasetTest < Test::Unit::TestCase
|
|
|
22
22
|
|
|
23
23
|
def test_get
|
|
24
24
|
hiv2 = 'M30502.1'
|
|
25
|
-
|
|
26
|
-
# EMBL Temporarily down, enable back whenever possible!
|
|
27
|
-
#{ embl: :ebi, nuccore: :ncbi }.each do |db, universe|
|
|
28
|
-
{ nuccore: :ncbi }.each do |db, universe|
|
|
25
|
+
{ embl: :ebi, nuccore: :ncbi }.each do |db, universe|
|
|
29
26
|
rd = MiGA::RemoteDataset.new(hiv2, db, universe)
|
|
30
27
|
assert_equal([hiv2], rd.ids)
|
|
31
28
|
|
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: 1.3.14.
|
|
4
|
+
version: 1.3.14.7
|
|
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: 2024-04-
|
|
11
|
+
date: 2024-04-24 00:00:00.000000000 Z
|
|
12
12
|
dependencies:
|
|
13
13
|
- !ruby/object:Gem::Dependency
|
|
14
14
|
name: daemons
|