miga-base 1.2.11.0 → 1.2.12.0
Sign up to get free protection for your applications and to get access to all the features.
- checksums.yaml +4 -4
- data/lib/miga/cli/action/download/gtdb.rb +1 -2
- data/lib/miga/dataset/result.rb +4 -1
- data/lib/miga/taxonomy.rb +2 -0
- data/lib/miga/version.rb +2 -2
- data/scripts/stats.bash +26 -1
- data/utils/requirements.txt +1 -0
- 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: 44cd40923e839969a12a0111a071a405d8cab376a0fa6e7102a21cafd33774a9
|
4
|
+
data.tar.gz: 5d1d0af6324b8c125a178b316a54e90eff2472aa7731407fc4d315a8b3fe9a36
|
5
5
|
SHA512:
|
6
|
-
metadata.gz:
|
7
|
-
data.tar.gz:
|
6
|
+
metadata.gz: 8f70cb028127bd30f5293005afaf73cf10c02a003cef1e027d85b3c6a2f61377e95be5962c03f6dd199f63da252160b21b7142c135a305aacb7f46b6551c90cf
|
7
|
+
data.tar.gz: 50a8676d741894e58a1b4c9b5f53ee665ff938e2814bf4570e204f26d38de7952aab1ee36c01a458021af3bba166432572d79f84f1b5fb430684bf9034506e97
|
@@ -28,7 +28,6 @@ module MiGA::Cli::Action::Download::Gtdb
|
|
28
28
|
|
29
29
|
def remote_list
|
30
30
|
cli.say 'Downloading genome list'
|
31
|
-
ds = {}
|
32
31
|
extra = ['sp_reps_only=' + cli[:reference].to_s]
|
33
32
|
json = MiGA::RemoteDataset.download(
|
34
33
|
:gtdb, :taxon, cli[:taxon], :genomes, nil, extra
|
@@ -49,7 +48,7 @@ module MiGA::Cli::Action::Download::Gtdb
|
|
49
48
|
end
|
50
49
|
|
51
50
|
def remote_row_name(asm)
|
52
|
-
acc =
|
51
|
+
acc = asm.to_s
|
53
52
|
acc.gsub!(/\.\d+\Z/, '') unless cli[:add_version]
|
54
53
|
acc.miga_name
|
55
54
|
end
|
data/lib/miga/dataset/result.rb
CHANGED
@@ -384,7 +384,10 @@ module MiGA::Dataset::Result
|
|
384
384
|
##
|
385
385
|
# Add result type +:stats+ at +base+ (no +_opts+ supported)
|
386
386
|
def add_result_stats(base, _opts)
|
387
|
-
|
387
|
+
add_files_to_ds_result(
|
388
|
+
MiGA::Result.new("#{base}.json"), name,
|
389
|
+
trna_list: '.trna.txt'
|
390
|
+
)
|
388
391
|
end
|
389
392
|
|
390
393
|
##
|
data/lib/miga/taxonomy.rb
CHANGED
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 = [1.2,
|
15
|
+
VERSION = [1.2, 12, 0].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(2022, 12,
|
23
|
+
VERSION_DATE = Date.new(2022, 12, 30)
|
24
24
|
|
25
25
|
##
|
26
26
|
# References of MiGA
|
data/scripts/stats.bash
CHANGED
@@ -9,7 +9,32 @@ DIR="$PROJECT/data/90.stats"
|
|
9
9
|
cd "$DIR"
|
10
10
|
|
11
11
|
# Initialize
|
12
|
-
miga date > "$DATASET.start"
|
12
|
+
miga date > "${DATASET}.start"
|
13
|
+
|
14
|
+
# tRNAscan-SE
|
15
|
+
fa="../05.assembly/${DATASET}.LargeContigs.fna"
|
16
|
+
if [[ -s "$fa" ]] ; then
|
17
|
+
d="$(miga ls -P "$PROJECT" -D "$DATASET" -m tax:d | awk '{print $2}')"
|
18
|
+
if [[ "$d" == "Bacteria" || "$d" == "Archaea" || "$d" == "Eukaryota" ]] ; then
|
19
|
+
dom_opt="-$(echo "$d" | perl -pe 's/(\S).*/$1/')"
|
20
|
+
out="${DATASET}.trna.txt"
|
21
|
+
# `echo O` is to avoid a hang from a pre-existing output file.
|
22
|
+
# This is better than pre-checking (and removing), because it avoids
|
23
|
+
# the (unlikely) scenario of a file racing (e.g., a file created right
|
24
|
+
# before tRNAscan-SE starts, or a `rm` failure).
|
25
|
+
#
|
26
|
+
# The trailing `|| true` is to treat failure as non-fatal
|
27
|
+
echo O | tRNAscan-SE $dom_opt -o "$out" -q "$fa" || true
|
28
|
+
if [[ -s "$out" ]] ; then
|
29
|
+
cnt=$(tail -n +4 "$out" | wc -l | awk '{print $1}')
|
30
|
+
aa="$(tail -n +4 "$out" | grep -v 'pseudo$' | awk '{print $5}' \
|
31
|
+
| grep -v 'Undet' | perl -pe 's/^f?([A-Za-z]+)[0-9]?/$1/' \
|
32
|
+
| sort | uniq | wc -l | awk '{print $1}')"
|
33
|
+
miga edit -P "$PROJECT" -D "$DATASET" \
|
34
|
+
-m "trna_count=Int($cnt),trna_aa=Int($aa)"
|
35
|
+
fi
|
36
|
+
fi
|
37
|
+
fi
|
13
38
|
|
14
39
|
# Calculate statistics
|
15
40
|
for i in raw_reads trimmed_fasta assembly cds essential_genes ssu distances taxonomy ; do
|
data/utils/requirements.txt
CHANGED
@@ -20,3 +20,4 @@ Fastp (reads) fastp https://github.com/OpenGene/fastp
|
|
20
20
|
Temurin (rdp) java https://adoptium.net/ Any Java VM would work
|
21
21
|
MyTaxa (mytaxa) MyTaxa http://enve-omics.ce.gatech.edu/mytaxa
|
22
22
|
Krona (mytaxa) ktImportText https://github.com/marbl/Krona/wiki
|
23
|
+
tRNAscan-SE tRNAscan-SE http://trna.ucsc.edu/tRNAscan-SE/ Required version: 2+
|
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: 1.2.
|
4
|
+
version: 1.2.12.0
|
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: 2022-12-
|
11
|
+
date: 2022-12-30 00:00:00.000000000 Z
|
12
12
|
dependencies:
|
13
13
|
- !ruby/object:Gem::Dependency
|
14
14
|
name: daemons
|