miga-base 0.7.12.2 → 0.7.13.0
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 +5 -5
- data/lib/miga/cli/action/derep_wf.rb +19 -10
- data/lib/miga/daemon.rb +2 -1
- data/lib/miga/version.rb +2 -2
- data/scripts/aai_distances.bash +11 -11
- data/scripts/ani_distances.bash +10 -10
- data/scripts/haai_distances.bash +11 -11
- metadata +4 -3
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
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---
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metadata.gz:
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data.tar.gz:
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SHA1:
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metadata.gz: 964b803e09887476153335589fad3d5aee2861ea
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data.tar.gz: ee0d34a4a7c8569d39bea4855a6054c57de78c81
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: b84efbc94fbfc848b85ae7c3cca7e26f2baea74c5f066a63cf1ede7fb26ed6c634f4c2e2cbe1c2752e54624cf48d6597b933474d4b4d6083cb505a3b17063cf5
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data.tar.gz: 0c7cfc6a149cab5fa1cfc5e386de789f84c132d227ad8ebbbc42dee2b076010bfe06b6697e69efe00a6639283c472f9ca3793a1e113506e691e50a182cfee2c6
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@@ -27,10 +27,13 @@ class MiGA::Cli::Action::DerepWf < MiGA::Cli::Action
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'--threshold FLOAT', Float,
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"Metric threshold (%) to dereplicate. By default: #{cli[:threshold]}"
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) { |v| cli[:threshold] = v }
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opt.on(
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'--quality',
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'Use genome with highest quality as clade representatives (default)'
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) { |v| cli[:criterion] = :quality }
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opt.on(
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'--medoids',
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'Use medoids as clade representatives'
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'By default: Use genome with the highest quality'
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'Use medoids as clade representatives'
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) { |v| cli[:criterion] = :medoids }
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opt.on(
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'--no-collection',
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@@ -47,12 +50,18 @@ class MiGA::Cli::Action::DerepWf < MiGA::Cli::Action
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def perform
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# Input data
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p = create_project(
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p = create_project(
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:assembly,
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{
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run_project_stats: false,
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run_clades: false,
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gsp_metric: cli[:metric],
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:"gsp_#{cli[:metric]}" => cli[:threshold]
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},
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{ run_mytaxa_scan: false, run_ssu: false }
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)
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unless cli[:threshold] >= 0.0 && cli[:threshold] <= 100.0
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raise
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raise 'The threshold of identity must be in the range [0,100]'
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end
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# Run
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private
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def dereplicate(p)
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cli.say
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r = p.result(:clade_finding) or raise
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cli.say 'Extracting genomospecies clades'
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r = p.result(:clade_finding) or raise 'Result unavailable: run failed'
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c_f = r.file_path(:clades_gsp) or raise 'Result incomplete: run failed'
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clades = File.readlines(c_f).map { |i| i.chomp.split("\t") }
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rep = representatives(p)
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end
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def representatives(p)
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cli.say
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cli.say 'Identifying representatives'
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f = File.expand_path('representatives.txt', cli[:outdir])
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if cli[:criterion] == :medoids
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FileUtils.cp(p.result(:clade_finding).file_path(:medoids_gsp), f)
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data/lib/miga/daemon.rb
CHANGED
data/lib/miga/version.rb
CHANGED
@@ -8,7 +8,7 @@ module MiGA
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# - Float representing the major.minor version.
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# - Integer representing gem releases of the current version.
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# - Integer representing minor changes that require new version number.
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VERSION = [0.7,
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VERSION = [0.7, 13, 0]
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##
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# Nickname for the current major.minor version.
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##
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# Date of the current gem release.
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VERSION_DATE = Date.new(2020, 7,
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VERSION_DATE = Date.new(2020, 7, 31)
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##
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# Reference of MiGA.
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data/scripts/aai_distances.bash
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@@ -13,17 +13,20 @@ echo -n "" > miga-project.log
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DS=$(miga ls -P "$PROJECT" --ref --no-multi --active)
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# Extract values
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echo "
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rm -f miga-project.txt
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(
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echo "metric a b value sd n omega" | tr " " "\\t"
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for i in $DS ; do
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echo "SELECT CASE WHEN omega!=0 THEN 'AAI' ELSE 'hAAI_AAI' END," \
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" seq1, seq2, aai, sd, n, omega from aai;" \
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| sqlite3 "$i.db" | tr "\\|" "\\t"
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echo "$i" >> miga-project.log
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done
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) | gzip -9c > miga-project.txt.gz
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# R-ify
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echo "
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aai <- read.table('miga-project.txt', sep='\\t', h=T, as.is=TRUE);
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aai <- read.table(gzfile('miga-project.txt.gz'), sep='\\t', h=T, as.is=TRUE);
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save(aai, file='miga-project.Rdata');
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if(sum(aai[,'a'] != aai[,'b']) > 0){
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h <- hist(aai[aai[,'a'] != aai[,'b'], 'value'], breaks=100, plot=FALSE);
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}
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" | R --vanilla
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# Gzip
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gzip -9 -f miga-project.txt
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# Finalize
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miga date > "miga-project.done"
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miga add_result -P "$PROJECT" -r "$SCRIPT" -f
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data/scripts/ani_distances.bash
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DS=$(miga ls -P "$PROJECT" --ref --no-multi --active)
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# Extract values
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echo "
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rm -f miga-project.txt
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(
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echo "metric a b value sd n omega" | tr " " "\\t"
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for i in $DS ; do
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echo "SELECT 'ANI', seq1, seq2, ani, sd, n, omega from ani ;" \
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| sqlite3 "$i.db" | tr "\\|" "\\t"
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echo "$i" >> miga-project.log
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done
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) | gzip -9c > miga-project.txt.gz
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# R-ify
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echo "
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ani <- read.table('miga-project.txt', sep='\\t', h=T, as.is=TRUE);
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ani <- read.table(gzfile('miga-project.txt.gz'), sep='\\t', h=T, as.is=TRUE);
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save(ani, file='miga-project.Rdata');
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if(sum(ani[,'a'] != ani[,'b']) > 0){
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h <- hist(ani[ani[,'a'] != ani[,'b'], 'value'], breaks=100, plot=FALSE);
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}
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" | R --vanilla
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# Gzip
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gzip -9 -f miga-project.txt
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# Finalize
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miga date > "miga-project.done"
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miga add_result -P "$PROJECT" -r "$SCRIPT" -f
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data/scripts/haai_distances.bash
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DS=$(miga ls -P "$PROJECT" --ref --no-multi --active)
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# Extract values
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echo "
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rm -f miga-project.txt
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(
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echo "metric a b value sd n omega" | tr " " "\\t"
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for i in $DS ; do
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echo "SELECT 'hAAI', seq1, seq2, aai, sd, n, omega from aai ;" \
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| sqlite3 "$i.db" | tr "\\|" "\\t"
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echo "$i" >> miga-project.log
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done
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) | gzip -9c > miga-project.txt.gz
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# R-ify
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echo "
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haai <- read.table('miga-project.txt', sep='\\t', h=T, as.is=TRUE);
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haai <- read.table(gzfile('miga-project.txt.gz'), sep='\\t', h=T, as.is=TRUE);
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save(haai, file='miga-project.Rdata');
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if(sum(haai[,'a'] != haai[,'b']) > 0){
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h <- hist(haai[haai[,'a'] != haai[,'b'], 'value'], breaks=100, plot=FALSE);
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write.table(
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cbind(h[['breaks']][-length(h[['breaks']])],
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h[['breaks']][-1],h[['counts']]),
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h[['breaks']][-1], h[['counts']]),
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file='miga-project.hist', quote=FALSE, sep='\\t',
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col.names=FALSE, row.names=FALSE);
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}
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" | R --vanilla
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# Gzip
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gzip -9 -f miga-project.txt
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# Finalize
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miga date > "miga-project.done"
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miga add_result -P "$PROJECT" -r "$SCRIPT" -f
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metadata
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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: 0.7.
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version: 0.7.13.0
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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: 2020-07-
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date: 2020-07-31 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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- !ruby/object:Gem::Version
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version: '0'
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requirements: []
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-
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rubyforge_project:
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rubygems_version: 2.5.2.3
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signing_key:
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specification_version: 4
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summary: MiGA
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