miga-base 0.2.2.1 → 0.2.2.2

data/scripts/essential_genes.bash

@@ -1,6 +1,7 @@
 #!/bin/bash
 # Available variables: $PROJECT, $RUNTYPE, $MIGA, $CORES
 set -e
+SCRIPT="essential"
 echo "MiGA: $MIGA"
 echo "Project: $PROJECT"
 source "$MIGA/scripts/miga.bash" || exit 1
@@ -8,6 +9,16 @@ cd "$PROJECT/data/07.annotation/01.function/01.essential"
 
 # Initialize
 date "+%Y-%m-%d %H:%M:%S %z" > "$DATASET.start"
+FAA="../../../06.cds/$DATASET.faa"
+
+# Check if there are any proteins
+if [[ ! -s $FAA ]] ; then
+  echo Empty protein set, bypassing essential genes
+  rm "$DATASET.start"
+  miga create_dataset -P "$PROJECT" -D $DATASET \
+    -m run_essential_genes=false --update
+  exit 0
+fi
 
 # Find and extract essential genes
 [[ -d "$DATASET.ess" ]] && rm -R "$DATASET.ess"
@@ -15,16 +26,15 @@ mkdir "$DATASET.ess"
 TYPE=$(miga list_datasets -P "$PROJECT" -D "$DATASET" \
    --metadata "type" | awk '{print $2}')
 if [[ "$TYPE" == "metagenome" || "$TYPE" == "virome" ]] ; then
-   HMM.essential.rb -i "../../../06.cds/$DATASET.faa" -o "$DATASET.ess.faa" \
+   HMM.essential.rb -i "$FAA" -o "$DATASET.ess.faa" \
       -m "$DATASET.ess/" -t "$CORES" -r "$DATASET" --metagenome \
       > "$DATASET.ess/log"
 else
-   HMM.essential.rb -i "../../../06.cds/$DATASET.faa" -o "$DATASET.ess.faa" \
+   HMM.essential.rb -i "$FAA" -o "$DATASET.ess.faa" \
       -m "$DATASET.ess/" -t "$CORES" -r "$DATASET" \
       > "$DATASET.ess/log"
 fi
 
 # Finalize
 date "+%Y-%m-%d %H:%M:%S %z" > "$DATASET.done"
-miga add_result -P "$PROJECT" -D "$DATASET" -r essential
-
+miga add_result -P "$PROJECT" -D "$DATASET" -r "$SCRIPT"

data/scripts/haai_distances.bash

@@ -1,6 +1,7 @@
 #!/bin/bash
 # Available variables: $PROJECT, $RUNTYPE, $MIGA, $CORES
 set -e
+SCRIPT="haai_distances"
 echo "MiGA: $MIGA"
 echo "Project: $PROJECT"
 source "$MIGA/scripts/miga.bash" || exit 1
@@ -15,32 +16,28 @@ DS=$(miga list_datasets -P "$PROJECT" --ref --no-multi)
 # Extract values
 echo "metric a b value sd n omega" | tr " " "\\t" >miga-project.txt
 for i in $DS ; do
-   echo "SELECT 'hAAI', seq1, seq2, aai, sd, n, omega from aai ;" \
-      | sqlite3 "$i.db" | tr "\\|" "\\t" >>miga-project.txt
-   echo "$i" >> miga-project.log
+  echo "SELECT 'hAAI', seq1, seq2, aai, sd, n, omega from aai ;" \
+    | sqlite3 "$i.db" | tr "\\|" "\\t" >>miga-project.txt
+  echo "$i" >> miga-project.log
 done
 
 # R-ify
-if true ; then
-  echo "
-  haai <- read.table('miga-project.txt', sep='\\t', h=T);
-  save(haai, file='miga-project.Rdata');"
-  if [[ $(cat miga-project.txt | wc -l) -gt 1 ]] ; then
-    echo "
-    h <- hist(haai[,'value'], breaks=100, plot=FALSE);
-    write.table(
-      cbind(h[['breaks']][-length(h[['breaks']])],
-        h[['breaks']][-1],h[['counts']]),
-      file='miga-project.hist', quote=FALSE, sep='\\t',
-      col.names=FALSE, row.names=FALSE);
-    "
-  fi
-fi | R --vanilla
+echo "
+haai <- read.table('miga-project.txt', sep='\\t', h=T, as.is=TRUE);
+save(haai, file='miga-project.Rdata');
+if(sum(haai[,'a'] != haai[,'b']) > 0){
+  h <- hist(haai[haai[,'a'] != haai[,'b'], 'value'], breaks=100, plot=FALSE);
+  write.table(
+    cbind(h[['breaks']][-length(h[['breaks']])],
+      h[['breaks']][-1],h[['counts']]),
+    file='miga-project.hist', quote=FALSE, sep='\\t',
+    col.names=FALSE, row.names=FALSE);
+}
+" | R --vanilla
 
 # Gzip
 gzip -9 -f miga-project.txt
 
 # Finalize
 date "+%Y-%m-%d %H:%M:%S %z" > "miga-project.done"
-miga add_result -P "$PROJECT" -r haai_distances
-
+miga add_result -P "$PROJECT" -r "$SCRIPT"

data/scripts/init.bash

@@ -106,7 +106,7 @@ echo "export PATH=\$MIGA_PATH\$PATH" >> "$HOME/.miga_rc"
 # Check for R packages
 echo "
 Looking for R packages:" >&2
-RLIBS="enveomics.R ape ggdendro ggplot2 gridExtra cluster dendextend vegan scatterplot3d"
+RLIBS="enveomics.R ape phangorn phytools ggdendro ggplot2 gridExtra cluster dendextend vegan scatterplot3d"
 for lib in $RLIBS ; do
    if ! check_rlib $lib ; then
       echo "+ Installing $lib" >&2

data/scripts/miga.bash

@@ -3,8 +3,14 @@ set -e
 #MIGA=${MIGA:-$(cd "$(dirname "$0")/.."; pwd)}
 source "$HOME/.miga_rc"
 export PATH="$MIGA/bin:$PATH"
+SCRIPT=${SCRIPT:-$(basename $0 .bash)}
 
 function exists { [[ -e "$1" ]] ; }
+function fx_exists { [[ $(type -t $1) == "function" ]] ; }
+
+for i in $(miga plugins -P "$PROJECT") ; do
+  source "$i/scripts-plugin.bash"
+done
 
 #if [[ "$RUNTYPE" == "qsub" ]] ; then
 #elif [[ "$RUNTYPE" == "msub" ]] ; then

data/scripts/mytaxa.bash

@@ -1,6 +1,7 @@
 #!/bin/bash
 # Available variables: $PROJECT, $RUNTYPE, $MIGA, $CORES
 set -e
+SCRIPT="mytaxa"
 echo "MiGA: $MIGA"
 echo "Project: $PROJECT"
 source "$MIGA/scripts/miga.bash" || exit 1
@@ -90,5 +91,4 @@ fi
 
 # Finalize
 date "+%Y-%m-%d %H:%M:%S %z" > "$DATASET.done"
-miga add_result -P "$PROJECT" -D "$DATASET" -r mytaxa
-
+miga add_result -P "$PROJECT" -D "$DATASET" -r "$SCRIPT"

data/scripts/mytaxa_scan.bash

@@ -1,6 +1,7 @@
 #!/bin/bash
 # Available variables: $PROJECT, $RUNTYPE, $MIGA, $CORES
 set -e
+SCRIPT="mytaxa_scan"
 echo "MiGA: $MIGA"
 echo "Project: $PROJECT"
 source "$MIGA/scripts/miga.bash" || exit 1
@@ -82,5 +83,4 @@ fi
 # Finalize
 rm -R "$TMPDIR"
 date "+%Y-%m-%d %H:%M:%S %z" > "$DATASET.done"
-miga add_result -P "$PROJECT" -D "$DATASET" -r mytaxa_scan
-
+miga add_result -P "$PROJECT" -D "$DATASET" -r "$SCRIPT"

data/scripts/ogs.bash

@@ -1,6 +1,7 @@
 #!/bin/bash
 # Available variables: $PROJECT, $RUNTYPE, $MIGA, $CORES
 set -e
+SCRIPT="ogs"
 echo "MiGA: $MIGA"
 echo "Project: $PROJECT"
 source "$MIGA/scripts/miga.bash" || exit 1
@@ -36,5 +37,4 @@ rm -rf miga-project.rbm
 
 # Finalize
 date "+%Y-%m-%d %H:%M:%S %z" > "miga-project.done"
-miga add_result -P "$PROJECT" -r ogs
-
+miga add_result -P "$PROJECT" -r "$SCRIPT"

data/scripts/read_quality.bash

@@ -1,6 +1,7 @@
 #!/bin/bash
 # Available variables: $PROJECT, $RUNTYPE, $MIGA, $CORES
 set -e
+SCRIPT="read_quality"
 echo "MiGA: $MIGA"
 echo "Project: $PROJECT"
 source "$MIGA/scripts/miga.bash" || exit 1
@@ -34,5 +35,4 @@ exists ../02.trimmed_reads/$b.[12].*.pdf \
 
 # Finalize
 date "+%Y-%m-%d %H:%M:%S %z" > "$DATASET.done"
-miga add_result -P "$PROJECT" -D "$DATASET" -r read_quality
-
+miga add_result -P "$PROJECT" -D "$DATASET" -r "$SCRIPT"

data/scripts/ssu.bash

@@ -1,6 +1,7 @@
 #!/bin/bash
 # Available variables: $PROJECT, $RUNTYPE, $MIGA, $CORES
 set -e
+SCRIPT="ssu"
 echo "MiGA: $MIGA"
 echo "Project: $PROJECT"
 source "$MIGA/scripts/miga.bash" || exit 1
@@ -32,5 +33,4 @@ fi
 
 # Finalize
 date "+%Y-%m-%d %H:%M:%S %z" > "$DATASET.done"
-miga add_result -P "$PROJECT" -D "$DATASET" -r ssu
-
+miga add_result -P "$PROJECT" -D "$DATASET" -r "$SCRIPT"

data/scripts/stats.bash

@@ -1,6 +1,7 @@
 #!/bin/bash
 # Available variables: $PROJECT, $RUNTYPE, $MIGA, $CORES, $DATASET
 set -e
+SCRIPT="stats"
 echo "MiGA: $MIGA"
 echo "Project: $PROJECT"
 source "$MIGA/scripts/miga.bash" || exit 1
@@ -12,11 +13,11 @@ cd "$DIR"
 date "+%Y-%m-%d %H:%M:%S %z" > "$DATASET.start"
 
 # Calculate statistics
-for i in raw_reads trimmed_fasta assembly cds ; do
+for i in raw_reads trimmed_fasta assembly cds essential_genes ; do
   echo "# $i"
   miga result_stats --compute-and-save -P "$PROJECT" -D "$DATASET" -r $i
 done
 
 # Finalize
 date "+%Y-%m-%d %H:%M:%S %z" > "$DATASET.done"
-miga add_result -P "$PROJECT" -D "$DATASET" -r stats
+miga add_result -P "$PROJECT" -D "$DATASET" -r "$SCRIPT"

data/scripts/subclades.bash

@@ -1,6 +1,7 @@
 #!/bin/bash
 # Available variables: $PROJECT, $RUNTYPE, $MIGA, $CORES
 set -e
+SCRIPT="subclades"
 echo "MiGA: $MIGA"
 echo "Project: $PROJECT"
 source "$MIGA/scripts/miga.bash" || exit 1
@@ -22,5 +23,4 @@ ruby "$MIGA/utils/subclades-compile.rb" . \
 
 # Finalize
 date "+%Y-%m-%d %H:%M:%S %z" > "miga-project.done"
-miga add_result -P "$PROJECT" -r subclades
-
+miga add_result -P "$PROJECT" -r "$SCRIPT"

data/scripts/trimmed_fasta.bash

@@ -1,6 +1,7 @@
 #!/bin/bash
 # Available variables: $PROJECT, $RUNTYPE, $MIGA, $CORES
 set -e
+SCRIPT="trimmed_fasta"
 echo "MiGA: $MIGA"
 echo "Project: $PROJECT"
 source "$MIGA/scripts/miga.bash" || exit 1
@@ -44,5 +45,4 @@ done
 
 # Finalize
 date "+%Y-%m-%d %H:%M:%S %z" > "$DATASET.done"
-miga add_result -P "$PROJECT" -D "$DATASET" -r trimmed_fasta
-
+miga add_result -P "$PROJECT" -D "$DATASET" -r "$SCRIPT"

data/scripts/trimmed_reads.bash

@@ -1,6 +1,7 @@
 #!/bin/bash
 # Available variables: $PROJECT, $RUNTYPE, $MIGA, $CORES
 set -e
+SCRIPT="trimmed_reads"
 echo "MiGA: $MIGA"
 echo "Project: $PROJECT"
 source "$MIGA/scripts/miga.bash" || exit 1
@@ -54,5 +55,4 @@ rm $b.[12].*.discard &>/dev/null
 
 # Finalize
 date "+%Y-%m-%d %H:%M:%S %z" > "$DATASET.done"
-miga add_result -P "$PROJECT" -D "$DATASET" -r trimmed_reads
-
+miga add_result -P "$PROJECT" -D "$DATASET" -r "$SCRIPT"

data/test/daemon_test.rb

@@ -72,7 +72,7 @@ class DaemonTest < Test::Unit::TestCase
     d.runopts(:latency, 0, true)
     assert_equal(0, d.latency)
     omit_if($jruby_tests, "JRuby doesn't implement fork.")
-    $child = fork { d.start }
+    $child = fork { d.start(["--shush"]) }
     sleep(3)
     dpath = File.expand_path("daemon/MiGA:#{p.name}",p.path)
     assert(File.exist?("#{dpath}.pid"))

data/test/test_helper.rb

@@ -1,5 +1,5 @@
-require "codeclimate-test-reporter"
-CodeClimate::TestReporter.start unless ENV["REMOTE_TESTS"].nil?
+require "simplecov"
+SimpleCov.start
 
 require "rubygems"
 require "test/unit"

data/utils/subclades-nj.R

@@ -0,0 +1,244 @@
+#!/usr/bin/env Rscript
+#
+# @package MiGA
+# @license Artistic-2.0
+#
+
+#= Load stuff
+argv <- commandArgs(trailingOnly=T)
+suppressPackageStartupMessages(library(ape))
+suppressPackageStartupMessages(library(vegan))
+suppressPackageStartupMessages(library(cluster))
+suppressPackageStartupMessages(library(phytools))
+suppressPackageStartupMessages(library(phangorn))
+suppressPackageStartupMessages(library(parallel))
+suppressPackageStartupMessages(library(enveomics.R))
+
+#= Main function
+subclades <- function(ani_file, out_base, thr=1, ani=c()) {
+  say("==> Out base:", out_base, "<==")
+  
+  # Input arguments
+  if(missing(ani_file)){
+    a <- as.data.frame(ani)
+  }else{
+    a <- read.table(gzfile(ani_file), sep="\t", header=TRUE, as.is=TRUE)
+  }
+  if(nrow(a)==0){
+    generate_empty_files(out_base)
+    return(NULL)
+  }
+  
+  # Get ANI distances
+  say("Distances")
+  a$d <- 1-a$value/100
+  ani.d <- enve.df2dist(data.frame(a$a, a$b, a$d), default.d=max(a$d)*1.2)
+  ani.ph <- midpoint(bionj(ani.d))
+  express.ori <- options('expressions')$expressions
+  if(express.ori < ani.ph$Nnode*4){
+    options(expressions=min(c(5e7,ani.ph$Nnode*4)))
+  }
+  write.tree(ani.ph, paste(out_base, ".nwk", sep=""))
+  options(expressions=express.ori)
+  ani.ph$edge.length[ ani.ph$edge.length<0 ] <- 0
+  ani.cpd <- cophenetic(ani.ph)
+  # Transform phylogenetic tree for clustering
+  ani.hcl <- as.hclust(
+    # 3. Randomly split multifurcations
+    multi2di(
+    # 2. Coalescent
+    compute.brtime(
+    # 1. Collapse zero-length and negative branches
+    di2multi(ani.ph, tol=min(ani.ph$edge.length[ani.ph$edge.length>0])))))
+  
+  # Silhouette
+  say("Silhouette")
+  k <- 2:min(length(labels(ani.d))-1, 100)
+  s <- sapply(k, function(x) {
+      library(cluster)
+      cl <- cutree(ani.hcl, k=x)
+      s <- silhouette(cl, dmatrix=ani.cpd)
+      c(mean(s[,'sil_width']),
+        -sum(ifelse(s[,'sil_width']>0,0,s[,'sil_width'])))
+    })
+  s.avg.z <- (s[1,]-mean(s[1,]))/(sd(s[1,])+0.0001)
+  s.neg.z <- (s[2,]-mean(s[2,]))/(sd(s[2,])+0.01)
+  ds <- s.avg.z - s.neg.z - 2/(1:length(k)) - (1:length(k))/50
+  top.n <- k[which.max(ds)]
+  
+  # Classify genomes
+  say("Classify => k :", top.n, "| n :", length(labels(ani.d)))
+  ani.types <- cutree(ani.hcl, k=top.n)
+  ani.medoids <- sapply(unique(ani.types),
+        clust.medoid, as.matrix(ani.d), ani.types)
+  
+  # Generate graphic report
+  say("Graphic report")
+  pdf(paste(out_base, ".pdf", sep=""), 7, 12)
+  layout(matrix(c(1,1,2,2,3,3,4,5),byrow=TRUE, ncol=2))
+  plot_distances(ani.d)
+  plot_silhouette(k, s[1,], s[2,], ds, top.n)
+  plot_clustering(ani.hcl, ani.d, ani.types, ani.medoids)
+  plot_tree(ani.ph, ani.types, ani.medoids)
+  dev.off()
+
+  # Save results
+  say("Text report")
+  write.table(ani.medoids, paste(out_base, "medoids", sep="."),
+    quote=FALSE, col.names=FALSE, row.names=FALSE)
+  save(ani.d, file=paste(out_base, "dist.rdata", sep="."))
+  classif <- cbind(names(ani.types), ani.types, ani.medoids[ ani.types ], NA)
+  ani.d.m <- 100 - as.matrix(ani.d)*100
+  for(j in 1:nrow(classif)){
+    classif[j,4] <- ani.d.m[classif[j,1], classif[j,3]]
+  }
+  write.table(classif, paste(out_base,"classif",sep="."),
+    quote=FALSE, col.names=FALSE, row.names=FALSE, sep="\t")
+
+  # Recursive search
+  say("Recursive search")
+  for(i in 1:top.n){
+    medoid <- ani.medoids[i]
+    ds_f <- names(ani.types)[ ani.types==i ]
+    say("Analyzing subclade", i, "with medoid:", medoid)
+    dir.create(paste(out_base, ".sc-", i, sep=""))
+    write.table(ds_f,
+      paste(out_base, ".sc-", i, "/miga-project.all",sep=""),
+      quote=FALSE, col.names=FALSE, row.names=FALSE)
+    if(length(ds_f) > 5){
+      a_f <- a[ (a$a %in% ds_f) & (a$b %in% ds_f), ]
+      subclades(out_base=paste(out_base, ".sc-", i, "/miga-project", sep=""),
+        thr=thr, ani=a_f)
+    }
+  }
+}
+
+#= Helper functions
+say <- function(...) { cat("[", date(), "]", ..., "\n") }
+
+generate_empty_files <- function(out_base) {
+  pdf(paste(out_base, ".pdf", sep=""), 7, 12)
+  plot(1, t="n", axes=F)
+  legend("center", "No data", bty="n")
+  dev.off()
+  file.create(paste(out_base,".1.classif",sep=""))
+  file.create(paste(out_base,".1.medoids",sep=""))
+}
+
+plot_silhouette <- function(k, s, ns, ds, top.n) {
+  # s
+  par(mar=c(4,5,1,5)+0.1)
+  plot(1, t="n", xlab="k (clusters)", ylab="", xlim=range(c(0,k)),
+    ylim=range(s), bty="n", xaxs="i", yaxt="n")
+  polygon(c(k[1], k, k[length(k)]), c(0,s,0), border=NA, col="grey80")
+  axis(2, fg="grey60", col.axis="grey60")
+  mtext("Mean silhouette", side=2, line=3, col="grey60")
+  # ns
+  par(new=TRUE)
+  plot(1, t="n", xlab="", xaxt="n", ylab="", yaxt="n", xlim=range(c(0,k)),
+    ylim=range(ns), bty="n", xaxs="i")
+  points(k, ns, type="o", pch=16, col=rgb(1/2,0,0,3/4))
+  axis(4, fg="darkred", col.axis="darkred")
+  mtext("Negative silhouette area", side=4, line=3, col="darkred")
+  # ds
+  par(new=TRUE)
+  plot(1, t="n", xlab="", xaxt="n", ylab="", yaxt="n", xlim=range(c(0,k)),
+    ylim=range(ds), bty="n", xaxs="i")
+  lines(k, ds)
+  abline(v=top.n, lty=2)
+}
+
+plot_distances <- function(dist) {
+  par(mar=c(5,4,1,2)+0.1)
+  hist(dist, border=NA, col="grey60", breaks=50, xlab="Distances", main="")
+}
+
+plot_clustering <- function(hcl, dist, types, medoids) {
+  par(mar=c(5,4,4,2)+0.1)
+  top.n <- length(medoids)
+  col <- ggplotColours(top.n)
+  plot(silhouette(types, dist=dist), col=col)
+  if(length(labels(dist))<=15){
+    plot(1, type="n", axes=FALSE, xlab="", ylab="", bty="n")
+    plot(1, type="n", axes=FALSE, xlab="", ylab="", bty="n")
+  }else{
+    ani.mds <- cmdscale(dist, k=4)
+    if(ncol(ani.mds)==4){
+      plot(ani.mds[,1], ani.mds[,2], col=col[types], cex=1/2,
+	xlab='Component 1', ylab='Component 2')
+      plot(ani.mds[,3], ani.mds[,4], col=col[types], cex=1/2,
+	xlab='Component 3', ylab='Component 4')
+    }else{
+      plot(1, type="n", axes=FALSE, xlab="", ylab="", bty="n")
+      plot(1, type="n", axes=FALSE, xlab="", ylab="", bty="n")
+    }
+  }
+}
+
+plot_tree <- function(phy, types, medoids){
+  layout(1)
+  top.n <- length(unique(types))
+  col <- ggplotColours(top.n)
+  is.medoid <- phy$tip.label %in% medoids
+  phy$tip.label[is.medoid] <- paste(phy$tip.label[is.medoid],
+    " [", types[phy$tip.label[is.medoid]], "]", sep='')
+  plot(phy, cex=ifelse(is.medoid, 1/3, 1/6),
+    font=ifelse(is.medoid, 2, 1),
+    tip.color=col[types[phy$tip.label]])
+}
+
+ggplotColours <- function(n=6, h=c(0, 360)+15, alpha=1){
+  if ((diff(h)%%360) < 1) h[2] <- h[2] - 360/n
+  hcl(h=seq(h[1], h[2], length=n), c=100, l=65, alpha=alpha)
+}
+
+# Modified from https://www.biostars.org/p/11987/
+clust.medoid <- function(i, distmat, clusters) {
+  ind <- (clusters == i)
+  if (sum(ind) <= 1){
+    return (rownames(distmat)[ind])
+  } else {
+    return(names(which.min(rowSums( distmat[ind, ind] ))))
+  }
+}
+
+# Code from http://grokbase.com/t/r/r-sig-phylo/109268tgx8/midpoint-rooting
+midpoint <- function(tree){
+  dm = cophenetic(tree)
+  tree = unroot(tree)
+  rn = max(tree$edge)+1
+  maxdm = max(dm)
+  ind = which(dm==maxdm,arr=TRUE)[1,]
+  tmproot = Ancestors(tree, ind[1], "parent")
+  tree = phangorn:::reroot(tree, tmproot)
+  edge = tree$edge
+  el = tree$edge.length
+  children = tree$edge[,2]
+  left = match(ind[1], children)
+  tmp = Ancestors(tree, ind[2], "all")
+  tmp= c(ind[2], tmp[-length(tmp)])
+  right = match(tmp, children)
+  if(el[left]>= (maxdm/2)){
+    edge = rbind(edge, c(rn, ind[1]))
+    edge[left,2] = rn
+    el[left] = el[left] - (maxdm/2)
+    el = c(el, maxdm/2)
+  }else{
+    sel = cumsum(el[right])
+    i = which(sel>(maxdm/2))[1]
+    edge = rbind(edge, c(rn, tmp[i]))
+    edge[right[i],2] = rn
+    eltmp = sel[i] - (maxdm/2)
+    el = c(el, el[right[i]] - eltmp)
+    el[right[i]] = eltmp
+  }
+  tree$edge.length = el
+  tree$edge=edge
+  tree$Nnode = tree$Nnode+1
+  phangorn:::reorderPruning(phangorn:::reroot(tree, rn))
+}
+
+#= Main
+subclades(ani_file=argv[1], out_base=argv[2],
+  thr=ifelse(is.na(argv[3]), 1, as.numeric(argv[3])))
+