miga-base 0.5.1.0 → 0.5.2.0
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- checksums.yaml +4 -4
- data/lib/miga/daemon.rb +1 -1
- data/lib/miga/version.rb +2 -2
- data/scripts/cds.bash +35 -6
- 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 +4 -3
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
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|
1
1
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---
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2
2
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SHA256:
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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: 5f447271e82d3343b44f79480c0133223af203dce8bb709ac7e389a559a4960f
|
4
|
+
data.tar.gz: fe31c84fe318692a636df5eb85f45e8cec7a1b05e399ebacbac16113e3b84a2a
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5
5
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SHA512:
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6
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-
metadata.gz:
|
7
|
-
data.tar.gz:
|
6
|
+
metadata.gz: 36f741d0157aa77e60d87fb6bd8bb5038923833a9ef4d40e405cb43b50f6b4ac88b24498e22a21c12987f933bbddd553ba6e01fc7435b1e4d838e9a7b55255fd
|
7
|
+
data.tar.gz: c4060a6f20c403c339ca161d721ee71c4e5a268703214a614b93be3c443021c4c954bc87e72587f96a0eb40b6cfe4b6234ab0d2bb4218e4cc686dff93d2aeccd
|
data/lib/miga/daemon.rb
CHANGED
@@ -203,7 +203,7 @@ class MiGA::Daemon < MiGA::MiGA
|
|
203
203
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else
|
204
204
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(job[:ds].nil? ? project : job[:ds]).add_result(job[:job], false).nil?
|
205
205
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end
|
206
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-
say "Completed pid:#{job[:pid]} for #{job[:task_name]}
|
206
|
+
say "Completed pid:#{job[:pid]} for #{job[:task_name]}" unless ongoing
|
207
207
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ongoing
|
208
208
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end
|
209
209
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# Avoid single datasets hogging resources
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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
|
# - Integer representing gem releases of the current version.
|
12
12
|
# - Integer representing minor changes that require new version number.
|
13
|
-
VERSION = [0.5,
|
13
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+
VERSION = [0.5, 2, 0]
|
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.
|
@@ -18,7 +18,7 @@ module MiGA
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|
18
18
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|
19
19
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##
|
20
20
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# Date of the current gem release.
|
21
|
-
VERSION_DATE = Date.new(2020, 1,
|
21
|
+
VERSION_DATE = Date.new(2020, 1, 7)
|
22
22
|
|
23
23
|
##
|
24
24
|
# Reference of MiGA.
|
data/scripts/cds.bash
CHANGED
@@ -17,14 +17,38 @@ if [[ -e "../05.assembly/$DATASET.LargeContigs.fna.gz" \
|
|
17
17
|
fi
|
18
18
|
|
19
19
|
# Run Prodigal
|
20
|
-
TYPE=$(miga
|
21
|
-
--metadata "type" | awk '{print $2}')
|
20
|
+
TYPE=$(miga ls -P "$PROJECT" -D "$DATASET" -m type | cut -f 2)
|
22
21
|
case "$TYPE" in
|
23
|
-
metagenome|virome)
|
24
|
-
|
22
|
+
metagenome|virome)
|
23
|
+
$CMD -p meta
|
24
|
+
prodigal -a "${DATASET}.faa" -d "${DATASET}.fna" -o "${DATASET}.gff3" \
|
25
|
+
-f gff -q -i "../05.assembly/${DATASET}.LargeContigs.fna" -p meta
|
26
|
+
;;
|
27
|
+
*)
|
28
|
+
P_LEN=0
|
29
|
+
BEST_CT=0
|
30
|
+
echo "# Codon table selection:" > "${DATASET}.ct.t"
|
31
|
+
for ct in 4 11 ; do
|
32
|
+
prodigal -a "${DATASET}.faa.$ct" -d "${DATASET}.fna.$ct" \
|
33
|
+
-o "${DATASET}.gff3.$ct" -f gff -q -p single -g "$ct" \
|
34
|
+
-i "../05.assembly/${DATASET}.LargeContigs.fna"
|
35
|
+
C_LEN=$(grep -v '^>' "${DATASET}.faa.$ct" \
|
36
|
+
| perl -pe 's/[^A-Z]//ig' | wc -c | awk '{print $1}')
|
37
|
+
echo "# codon table $ct total length: $C_LEN aa" \
|
38
|
+
>> "${DATASET}.ct.t"
|
39
|
+
if [[ $C_LEN > $P_LEN ]] ; then
|
40
|
+
for x in faa fna gff3 ; do
|
41
|
+
mv "${DATASET}.$x.$ct" "${DATASET}.$x"
|
42
|
+
done
|
43
|
+
P_LEN=$C_LEN
|
44
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+
BEST_CT=$ct
|
45
|
+
else
|
46
|
+
rm "$DATASET".*."$ct"
|
47
|
+
fi
|
48
|
+
done
|
49
|
+
echo "# Selected table: $BEST_CT"
|
50
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+
;;
|
25
51
|
esac
|
26
|
-
prodigal -a "$DATASET.faa" -d "$DATASET.fna" -f gff -o "$DATASET.gff3" \
|
27
|
-
-p $PROCEDURE -q -i "../05.assembly/$DATASET.LargeContigs.fna"
|
28
52
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|
29
53
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# Clean Prodigal noisy deflines
|
30
54
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for i in faa fna ; do
|
@@ -34,6 +58,10 @@ done
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|
34
58
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perl -pe 's/ID=([0-9]+_[0-9]+);/ID=gene_$1;/' "$DATASET.gff3" \
|
35
59
|
> "$DATASET.gff3.t"
|
36
60
|
mv "$DATASET.gff3.t" "$DATASET.gff3"
|
61
|
+
if [[ -e "${DATASET}.ct.t" ]] ; then
|
62
|
+
cat "${DATASET}.ct.t" >> "${DATASET}.gff3"
|
63
|
+
rm "${DATASET}.ct.t"
|
64
|
+
fi
|
37
65
|
|
38
66
|
# Gzip
|
39
67
|
for ext in gff3 faa fna ; do
|
@@ -43,3 +71,4 @@ done
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|
43
71
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# Finalize
|
44
72
|
miga date > "$DATASET.done"
|
45
73
|
miga add_result -P "$PROJECT" -D "$DATASET" -r "$SCRIPT" -f
|
74
|
+
|
@@ -1 +1 @@
|
|
1
|
-
|
1
|
+
utils/enveomics/Pipelines/assembly.pbs/../../Scripts/FastA.N50.pl
|
@@ -1 +1 @@
|
|
1
|
-
|
1
|
+
utils/enveomics/Pipelines/assembly.pbs/../../Scripts/FastA.filterN.pl
|
@@ -1 +1 @@
|
|
1
|
-
|
1
|
+
utils/enveomics/Pipelines/assembly.pbs/../../Scripts/FastA.length.pl
|
@@ -1 +1 @@
|
|
1
|
-
|
1
|
+
utils/enveomics/Pipelines/blast.pbs/../../Scripts/FastA.split.pl
|
@@ -1 +1 @@
|
|
1
|
-
|
1
|
+
utils/enveomics/Scripts/lib/../../enveomics.R
|
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: 0.5.
|
4
|
+
version: 0.5.2.0
|
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: 2020-01-
|
11
|
+
date: 2020-01-07 00:00:00.000000000 Z
|
12
12
|
dependencies:
|
13
13
|
- !ruby/object:Gem::Dependency
|
14
14
|
name: daemons
|
@@ -515,7 +515,8 @@ required_rubygems_version: !ruby/object:Gem::Requirement
|
|
515
515
|
- !ruby/object:Gem::Version
|
516
516
|
version: '0'
|
517
517
|
requirements: []
|
518
|
-
|
518
|
+
rubyforge_project:
|
519
|
+
rubygems_version: 2.7.6
|
519
520
|
signing_key:
|
520
521
|
specification_version: 4
|
521
522
|
summary: MiGA
|