miga-base 0.3.9.0 → 0.3.9.1

data/utils/enveomics/Scripts/GFF.catsbj.pl

@@ -0,0 +1,127 @@
+#!/usr/bin/env perl
+
+# @author  Luis M. Rodriguez-R
+# @license Artistic-2.0
+
+use warnings;
+use strict;
+use List::Util qw/min max/;
+use Getopt::Std;
+
+sub HELP_MESSAGE { die "
+
+Description:
+  Generates a list of coordinates from a GFF table concatenating the subject
+  sequences.
+  
+  See also: BlastTab.recplot2.R and BlastTab.catsbj.pl
+
+Usage:
+  $0 [options] seq.fa map.gff > abs-coords.tsv
+
+  seq.fa	Subject sequences (contigs) in FastA format.
+  map.gff	Features to map in GFF.
+   
+  Options:
+  -L path       Generate a file with the absolute coordinates of the
+                concatenated contigs. This is identical to the .lim file
+                generated by BlastTab.catsbj.pl.
+  -i            Preserve exact coordinates and include inter-feature windows as
+                separate bins. By default, the coordinates are set in the
+                midpoint between features when non-contiguous.
+  -s		The FastA provided is to be treated as a subset of the subject.
+   		By default, it expects all the contigs to be present in the
+		BLAST.
+  -q		Run quietly.
+  -h		Display this message and exit.
+   
+"; }
+
+my %o;
+getopts('L:isqh', \%o);
+my($fa, $map) = @ARGV;
+($fa and $map) or &HELP_MESSAGE;
+$o{h} and &HELP_MESSAGE;
+
+my %seq = ();
+my @seq = ();
+my $tot = 0;
+
+SEQ:{
+  print STDERR "== Reading reference sequences\n" unless $o{q};
+  open FA, "<", $fa or die "Cannot read the file: $fa: $!\n";
+  my $cur_seq = '';
+  while(<FA>){
+    chomp;
+    if(m/^>(\S+)/){
+      my $c = $1;
+      $seq{$c} = exists $seq{$cur_seq} ? $seq{$cur_seq}+1 : 1;
+      push @seq, $c;
+      $cur_seq = $c;
+    }else{
+      s/[^A-Za-z]//g;
+      $seq{$cur_seq} += length $_;
+    }
+  }
+  close FA;
+  print STDERR " Found ".(scalar @seq)." sequences.\n" unless $o{q};
+}
+
+$o{L} ||= '/dev/null';
+open LIM, ">", $o{L} or die "Cannot create the file: $o{L}: $!\n";
+my $l = 0;
+for my $s (@seq){
+  print LIM "$s\t".(++$l)."\t$seq{$s}\n";
+  ($l, $seq{$s}) = ($seq{$s}, $l);
+}
+close LIM;
+
+MAP: {
+  print STDERR "== Reading mapping\n" unless $o{q};
+  open GFF, "<", $map or die "Cannot read the file: $map: $!\n";
+  my $last_end = 1;
+  my $last_name = "NA";
+  print "1\tNA\tNA\n";
+  my $i = 0;
+  FEATURE: while(<GFF>){
+    next if /^\s*(#.*)?$/; # Blank or comment lines
+    chomp;
+    my @ln = split /\t/;
+    $ln[4] or die "Cannot parse line $map:$.: $_\n";
+    unless(exists $seq{$ln[0]}){
+      die "Cannot find the subject sequence: $ln[0]\n" unless $o{s};
+      next FEATURE;
+    }
+    $i++;
+    my $start = $seq{$ln[0]}+$ln[3];
+    my $end   = $seq{$ln[0]}+$ln[4];
+    my $name  = "feat_$i";
+    if($ln[8] =~ /^gene_id=(\d+)/){ # <- GeneMark style
+      $name = "gene_id_$1";
+    }elsif($ln[8] =~ /^ID=\d+_(\d+)/){ # <- Prodigal style
+      $name = $ln[0]."_".$1;
+    }elsif($ln[8] =~ /^ID=([^;]+)/){
+      $name = $1;
+    }
+    if($o{i}){
+      $start = $last_end if $start < $last_end;
+      print "$start\t$last_name~$name\tGAP\n" unless $start==$last_end;
+      print "$end\t$name\tFEAT\n";
+    }else{
+      my $midpoint = int(($last_end + $start)/2);
+      print "$last_end\t$last_name\tFEAT\n" unless $last_end==1;
+    }
+    $last_name = $name;
+    $last_end = $end;
+  }
+  if($last_end > 1){
+    if($o{i}){
+      print "$l\t$last_name~NA\tGAP\n" unless $last_end==$l;
+    }else{
+      print "$l\t$last_name\tFEAT\n";
+    }
+  }
+  close GFF;
+  print STDERR " done.\n" unless $o{q};
+}
+

data/utils/enveomics/Scripts/aai.rb

@@ -261,7 +261,8 @@ Dir.mktmpdir do |dir|
       # Nothing to do
     when "diamond"
       `"#{o[:bin]}diamond" makedb --in "#{dir}/#{seq}.fa" \
-      --db "#{dir}/#{seq}.fa.dmnd" --threads "#{o[:thr]}"`
+      --db "#{dir}/#{seq}.fa.dmnd" --threads "#{o[:thr]}" \
+      --quiet`
     else
       abort "Unsupported program: #{o[:program]}."
     end
@@ -297,9 +298,9 @@ Dir.mktmpdir do |dir|
       `sort -k 1 "#{dir}/#{i}.tab.uns" > "#{dir}/#{i}.tab"`
     when "diamond"
       `"#{o[:bin]}diamond" blastp --threads "#{o[:thr]}" --db "#{s}.dmnd" \
-      --query "#{q}" --sensitive --daa "#{dir}/#{i}.daa" \
+      --query "#{q}" --sensitive --daa "#{dir}/#{i}.daa" --quiet \
       && "#{o[:bin]}diamond" view --daa "#{dir}/#{i}.daa" --outfmt 6 \
-      --out "#{dir}/#{i}.tab"`
+      --out "#{dir}/#{i}.tab" --quiet`
     else
       abort "Unsupported program: #{o[:program]}."
     end

data/utils/enveomics/Scripts/lib/enveomics.R

@@ -1 +1 @@
-../../enveomics.R
+utils/enveomics/Scripts/lib/../../enveomics.R

data/utils/enveomics/enveomics.R/DESCRIPTION

@@ -1,5 +1,5 @@
 Package: enveomics.R
-Version: 1.3
+Version: 1.4.4
 Authors@R: c(person("Luis M.","Rodriguez-R",role=c("aut","cre"),
 	   email="lmrodriguezr@gmail.com"))
 Title: Various Utilities for Microbial Genomics and Metagenomics
@@ -15,7 +15,6 @@ Depends:
    stats,
    methods,
    parallel,
-   modeest,
    fitdistrplus,
    sn,
    investr

data/utils/enveomics/enveomics.R/NAMESPACE

@@ -1,5 +1,4 @@
 import(methods)
-import(modeest)
 import(parallel)
 import(fitdistrplus)
 import(sn)
@@ -33,7 +32,8 @@ export(
   enve.recplot2.findPeaks.emauto, enve.recplot2.findPeaks.em,
   enve.recplot2.findPeaks.mower,
   enve.recplot2.corePeak, enve.recplot2.changeCutoff,
-  enve.recplot2.extractWindows, enve.recplot2.compareIdentities,
+  enve.recplot2.windowDepthThreshold, enve.recplot2.extractWindows,
+  enve.recplot2.compareIdentities,
   enve.recplot2.coordinates, enve.recplot2.seqdepth, enve.recplot2.ANIr,
   enve.growthcurve, plot.enve.GrowthCurve, summary.enve.GrowthCurve,
-  enve.col2alpha)
+  enve.col2alpha, enve.truncate)

data/utils/enveomics/enveomics.R/R/recplot.R

@@ -55,7 +55,7 @@ enve.recplot <- structure(function(
 	ret.recplot=FALSE,
 	### Indicates if the matrix of the recruitment plot is to be returned.
 	ret.hist=FALSE,
-	### Indicates if the vectors of the identity and position histograms are to be returned.
+	### Ignored, for backwards compatibility.
 	ret.mode=FALSE,
 	### Indicates if the mode of the identity is to be computed. It requires the modeest
 	### package.
@@ -205,7 +205,6 @@ enve.recplot <- structure(function(
    legend('bottomright', paste(id.shortname, 'histogram'), bg=rgb(1,1,1,2/3));
    out <- c(out, list(id.mean=mean(rec[, id.reccol])));
    out <- c(out, list(id.median=median(rec[, id.reccol])));
-   if(ret.mode)   out <- c(out, list(id.mode=modeest::mlv(rec[, id.reccol], method='mfv')$M));
    if(ret.hist)  out <- c(out, list(id.hist=id.hist));
 
    # Position histogram
@@ -287,7 +286,7 @@ enve.recplot <- structure(function(
    ### 
    ### id.median: Median identity.
    ### 
-   ### id.mode (if ret.mode=TRUE): Mode of the identity.
+   ### id.mode (if ret.mode=TRUE): Mode of the identity. Deprecated.
    ### 
    ### id.hist (if ret.hist=TRUE): Values of the identity histogram.
    ###