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 CHANGED
@@ -1,7 +1,7 @@
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  ---
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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',
@@ -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(:assembly,
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- { run_project_stats: false, run_clades: false,
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- gsp_metric: cli[:metric], :"gsp_#{cli[:metric]}" => cli[:threshold] },
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- { run_mytaxa_scan: false, run_ssu: false })
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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 "The threshold of identity must be in the range [0,100]"
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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
@@ -65,8 +74,8 @@ class MiGA::Cli::Action::DerepWf < MiGA::Cli::Action
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  private
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  def dereplicate(p)
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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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+ 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)
@@ -87,7 +96,7 @@ class MiGA::Cli::Action::DerepWf < MiGA::Cli::Action
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  end
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  def representatives(p)
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- cli.say "Identifying representatives"
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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)
@@ -91,7 +91,8 @@ class MiGA::Daemon < MiGA::MiGA
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  flush!
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  if (loop_i % 12).zero?
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  purge!
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- recalculate_status!
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+ # TEMPORARILY DISABLED:
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+ # recalculate_status!
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  end
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  save_status
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  sleep(latency)
@@ -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, 12, 2]
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+ VERSION = [0.7, 13, 0]
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  ##
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  # Nickname for the current major.minor version.
@@ -16,7 +16,7 @@ module MiGA
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  ##
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  # Date of the current gem release.
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- VERSION_DATE = Date.new(2020, 7, 24)
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+ VERSION_DATE = Date.new(2020, 7, 31)
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  ##
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  # Reference of MiGA.
@@ -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 "metric a b value sd n omega" | tr " " "\\t" >miga-project.txt
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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" >>miga-project.txt
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- echo "$i" >> miga-project.log
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- done
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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 "$i" >> miga-project.log
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+ done
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+ ) | gzip -9c > miga-project.txt.gz
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  # R-ify
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  echo "
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- aai <- read.table('miga-project.txt', sep='\\t', h=T, as.is=TRUE);
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+ aai <- read.table(gzfile('miga-project.txt.gz'), sep='\\t', h=T, as.is=TRUE);
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  save(aai, file='miga-project.Rdata');
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  if(sum(aai[,'a'] != aai[,'b']) > 0){
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  h <- hist(aai[aai[,'a'] != aai[,'b'], 'value'], breaks=100, plot=FALSE);
@@ -35,9 +38,6 @@ if(sum(aai[,'a'] != aai[,'b']) > 0){
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  }
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  " | R --vanilla
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- # Gzip
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- gzip -9 -f miga-project.txt
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-
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  # Finalize
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  miga date > "miga-project.done"
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  miga add_result -P "$PROJECT" -r "$SCRIPT" -f
@@ -13,16 +13,19 @@ echo -n "" > miga-project.log
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  DS=$(miga ls -P "$PROJECT" --ref --no-multi --active)
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  # Extract values
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- echo "metric a b value sd n omega" | tr " " "\\t" >miga-project.txt
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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" >>miga-project.txt
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- echo "$i" >> miga-project.log
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- done
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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 "$i" >> miga-project.log
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+ done
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+ ) | gzip -9c > miga-project.txt.gz
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  # R-ify
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  echo "
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- ani <- read.table('miga-project.txt', sep='\\t', h=T, as.is=TRUE);
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+ ani <- read.table(gzfile('miga-project.txt.gz'), sep='\\t', h=T, as.is=TRUE);
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  save(ani, file='miga-project.Rdata');
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  if(sum(ani[,'a'] != ani[,'b']) > 0){
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  h <- hist(ani[ani[,'a'] != ani[,'b'], 'value'], breaks=100, plot=FALSE);
@@ -34,9 +37,6 @@ if(sum(ani[,'a'] != ani[,'b']) > 0){
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  }
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  " | R --vanilla
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- # Gzip
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- gzip -9 -f miga-project.txt
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-
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  # Finalize
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  miga date > "miga-project.done"
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  miga add_result -P "$PROJECT" -r "$SCRIPT" -f
@@ -17,30 +17,30 @@ echo -n "" > miga-project.log
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  DS=$(miga ls -P "$PROJECT" --ref --no-multi --active)
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  # Extract values
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- echo "metric a b value sd n omega" | tr " " "\\t" >miga-project.txt
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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" >>miga-project.txt
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- echo "$i" >> miga-project.log
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- done
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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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29
 
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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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43
 
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- # Gzip
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- gzip -9 -f miga-project.txt
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-
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  # Finalize
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45
  miga date > "miga-project.done"
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  miga add_result -P "$PROJECT" -r "$SCRIPT" -f
metadata CHANGED
@@ -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: 0.7.12.2
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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: 2020-07-24 00:00:00.000000000 Z
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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
@@ -560,7 +560,8 @@ required_rubygems_version: !ruby/object:Gem::Requirement
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  - !ruby/object:Gem::Version
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  version: '0'
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  requirements: []
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- rubygems_version: 3.1.2
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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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566
  specification_version: 4
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  summary: MiGA