miga-base 1.3.20.1 → 1.3.20.3
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/cds.bash +11 -1
- metadata +2 -2
checksums.yaml
CHANGED
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@@ -1,7 +1,7 @@
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1
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---
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SHA256:
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-
metadata.gz:
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-
data.tar.gz:
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3
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metadata.gz: c6cd171c44ec3139121607db27badddcd12e8cefd45f49acc6bc5f018184943f
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4
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data.tar.gz: 8ca59c51be7224fb7e0d3b0561cb72ef9f95594a2b51fa9a3c04c65ab60d7b66
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SHA512:
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-
metadata.gz:
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7
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data.tar.gz:
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6
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metadata.gz: 281aa0434dbeb5d4d5c69e5df44a459e77d22ce1664c68553fe61c04640ec27128002428aaffca3f1913973d2cb689afba51e683f7e3ca594bfede38b1ad79be
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7
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data.tar.gz: 2f37a8bc9fd5e516a669185b56e71339fca60314d7505917e1c4d4291801c81f4d9a3a36988e63bf0e0829d63046b3dc1b34c072a893449df2b63aa849cb1a05
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data/lib/miga/version.rb
CHANGED
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@@ -12,7 +12,7 @@ module MiGA
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# - String indicating release status:
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# - rc* release candidate, not released as gem
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# - [0-9]+ stable release, released as gem
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-
VERSION = [1.3, 20,
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+
VERSION = [1.3, 20, 3].freeze
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##
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# Nickname for the current major.minor version.
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@@ -20,7 +20,7 @@ module MiGA
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##
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# Date of the current gem relese.
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-
VERSION_DATE = Date.new(2024,
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VERSION_DATE = Date.new(2024, 8, 29)
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##
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# References of MiGA
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data/scripts/cds.bash
CHANGED
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@@ -16,6 +16,14 @@ if [[ -e "../05.assembly/$DATASET.LargeContigs.fna.gz" \
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miga add_result -P "$PROJECT" -D "$DATASET" -r assembly -f
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fi
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# Check if the input assembly is empty
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ASM_LEN=$(grep -v '^>' "../05.assembly/${DATASET}.LargeContigs.fna" \
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| wc -lc | awk '{ print $2-$1 }')
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if [[ "$ASM_LEN" -lt 1 ]] ; then
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miga edit -P "$PROJECT" -D "$DATASET" --inactivate "Empty assembly"
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exit 0
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fi
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# Run Prodigal
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TYPE=$(miga ls -P "$PROJECT" -D "$DATASET" -m type | cut -f 2)
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case "$TYPE" in
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@@ -26,10 +34,12 @@ case "$TYPE" in
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*)
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P_LEN=0
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BEST_CT=0
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PROCEDURE=single
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[[ "$ASM_LEN" -lt 2000 ]] && PROCEDURE=meta
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echo "# Codon table selection:" > "${DATASET}.ct.t"
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for ct in 11 4 ; do
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prodigal -a "${DATASET}.faa.$ct" -d "${DATASET}.fna.$ct" \
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-
-o "${DATASET}.gff3.$ct" -f gff -q -p
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-o "${DATASET}.gff3.$ct" -f gff -q -p $PROCEDURE -g "$ct" \
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-i "../05.assembly/${DATASET}.LargeContigs.fna"
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C_LEN=$(grep -v '^>' "${DATASET}.faa.$ct" \
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| perl -pe 's/[^A-Z]//ig' | wc -c | awk '{print $1}')
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metadata
CHANGED
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@@ -1,14 +1,14 @@
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--- !ruby/object:Gem::Specification
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name: miga-base
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version: !ruby/object:Gem::Version
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-
version: 1.3.20.
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version: 1.3.20.3
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platform: ruby
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authors:
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- Luis M. Rodriguez-R
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autorequire:
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bindir: bin
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cert_chain: []
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date: 2024-
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date: 2024-08-29 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: daemons
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