miga-base 0.7.25.2 → 0.7.25.3

data/utils/enveomics/Scripts/Newick.autoprune.R

@@ -1,27 +0,0 @@
-#!/usr/bin/env Rscript
-#
-# @author  Luis M. Rodriguez-R
-# @update  Jan-07-2016
-# @license artistic license 2.0
-#
-
-#= Load stuff
-args <- commandArgs(trailingOnly = F)  
-enveomics_R <- file.path(dirname(
-   sub("^--file=", "", args[grep("^--file=", args)])),
-   "lib", "enveomics.R")
-source(file.path(enveomics_R, "R", "cliopts.R"))
-source(file.path(enveomics_R, "R", "autoprune.R"))
-
-#= Generate interface
-opt <- enve.cliopts(enve.prune.dist,
-   file.path(enveomics_R, "man", "enve.prune.dist.Rd"),
-   positional_arguments=1,
-   usage="usage: %prog [options] output.nwk",
-   mandatory=c("t"),
-   number=c("min_dist","order"),
-   o_desc=list(t="A tree to prune in Newick format."))
-
-#= Run it!
-pt <- do.call("enve.prune.dist", opt$options)
-ape::write.tree(pt, opt$args[1])

data/utils/enveomics/Scripts/RAxML-EPA.to_iToL.pl

@@ -1,228 +0,0 @@
-#!/usr/bin/env perl
-
-# @author Luis M Rodriguez-R <lmrodriguezr at gmail dot com>
-# @update Mar-23-2015
-# @license Artistic License 2.0
-
-use warnings;
-use strict;
-use List::Util qw/sum max/;
-use Getopt::Std;
-use Math::Round qw/round/;
-our $VERSION = 1.1;
-
-warn <<WARN
-
-
-┌──[ IMPORTANT ]─────────────────────────────────────────────────┐
-│ This script has been deprecated in favor of JPlace.to_iToL.rb. │
-│ Please use the new version, together with the RAxML EPA's file │
-│ RAxML_portableTree.*.jplace instead.                           │
-└────────────────────────────────────────────────────────────────┘
-WARN
-;
-sub HELP_MESSAGE {
-die "
-Description:
-   Reformats the node names (labels) of a RAxML_originalLabelledTree.<NAME> file
-   (produced by RAxML's EPA, -f v), so it can be opened in most tree viewers (like
-   iToL and FigTree).  Also, it creates iToL-compatible files to draw pie-charts
-   (based on the classification of short reads) in the nodes of the reference tree.
-
-Usage:
-   $0 -n <NAME> [other options...]
-
-   -n <str> *	Name of the run used in RAxML.
-   -t <str>	Use this file as original labelled tree, instead of generating one
-   		based on the job name.  By default, RAxML_originalLabelledTree.<NAME>
-		in the -d directory. See [NOTE1].
-   -d <str>	Directory containing RAxML files.  By default: current directory.
-   -o <str>	Output tree.  By default, it takes the path to the input tree and
-   		appends .nwk to it.
-   -l <str>	File containing a list of internal nodes.  The nodes in the list
-   		will be renamed, and the reads of all children nodes will be
-		transferred to it.  This can be useful if you want to display
-		these nodes collapsed.  The format of the file is raw text, with
-		two columns separated by tabs or spaces, where the first column is
-		the original name of the internal node (without the brackets) and
-		the second is the name to be used.  See [NOTE2].
-   -a		Append original label to the renamed nodes (only if -l is passed).
-   -s <str>	The names of the reads will be assumed to contain the sample name,
-   		separated by this string.  For example, if the value is '_', and
-		a read has the name 'hco_ABCDEF/1#ACTG', it will be assumed to be
-		a read from the sample 'hco'.  If not provided, all the reads are
-		assumed to come from the same sample (called 'unknown').
-   -m <str>	Comma-delimited list of samples.  If not provided, all found samples
-   		will be used (unsorted).
-   -c <str>	Comma-delimited list of colors (in RGB hexadecimal) to represent
-   		the different samples.  If not provided (or if insufficient values
-		are provided) random colors are generated.
-   -N <str>	Comma-delimited list of normalizing factors per dataset.  Typically,
-   		the size of the datasets divided by a fixed value (e.g. size x 1,000,
-		to express sizes as reads per thousand).
-   -T		Use the total number of assigned reads per sample (times a constant)
-   		as the normalizing factor. The constant used corresponds to the 100
-		times the size of the largest factor. If passed, -N is ignored.
-   -q		Run quietly.
-   -h/--help	Displays this message and exits.
-
-   * Mandatory
-   [NOTE1] The tree provided by -t MUST be based on a tree produced by this script
-   without the -l option.
-   [NOTE2] The tree produced by RAxML-EPA is usually not correctly rooted, which
-   makes the -l option useless.  However, you can manually root the tree and provide
-   the rooted tree in Newick format using the -t option.  If you do this, make
-   sure the program doesn't change/delete the names of the internal nodes.  I know
-   that iToL can do it correctly (if you export preserving the original IDs), while
-   FigTree deletes the labels.  I didn't try any other tool.
-
-";
-}
-
-my %o;
-getopts('n:t:d:o:l:s:m:c:N:Tqh', \%o);
-$o{d} ||= '.';
-$o{n} or &HELP_MESSAGE;
-$o{h} and &HELP_MESSAGE;
-$o{c} = [split /,/, (defined $o{c}?$o{c}:"")];
-$o{N} = [split /,/, (defined $o{N}?$o{N}:"")];
-
-# Set files
-my $inTree   = ($o{t} || $o{d}."/RAxML_originalLabelledTree.".$o{n});
-my $outTree  = ($o{o} || $inTree.".nwk");
-my $inClass  = $o{d}."/RAxML_classification.".$o{n};
-my $outClass = $inClass.".iToL";
-my $outColl  = $outTree.".collapse.iToL";
-
-# Relocate tree node names
-print STDERR "o Reformatting tree.\n" unless $o{q};
-open INTREE, "<", $inTree or die "Cannot read file: $inTree: $!\n";
-my $tree = <INTREE>;
-$tree =~ s/:([\d\.]+)(\[.+?\])/$2:$1/g unless $o{t};
-close INTREE;
-
-# Read leaf nodes
-print STDERR "o Reading nodes.\n" unless $o{q};
-my %tags    = ();
-
-my $t = $tree;
-while($t =~ m/([A-Za-z0-9_\|\.-]+\[([A-Za-z0-9_\|\.-]+)\])/){
-   my $n = $1;
-   my $ta = $2;
-   $tags{$ta} = $n;
-   $t = substr $t, (length($n) + index $t, $n);
-}
-
-# Label/collapse internal nodes
-if($o{l}){
-   print STDERR "o Labeling/collapsing internal nodes.\n";
-   open LIST, "<", $o{l} or die "Cannot read file: $o{l}: $!\n";
-   open COLL, ">", $outColl or die "Cannot create file: $outColl: $!\n";
-   while(<LIST>){
-      chomp;
-      next if /^#/ or /^\s*$/;
-      # Label internal node
-      my @l = split /\s+/;
-      $l[0] =~ m/^\[(.+)\]$/ or die "Unable to parse internal node name: $l[0].\n";
-      my $ori = $1;
-      my $new = $l[1];
-      if(exists $tags{$ori}){
-	 warn "Warning: Trying to label/collapse $ori as $new, already defined as $tags{$ori}.\n";
-	 next;
-      }
-      $new =~ s/[^A-Za-z0-9_\|\.\-]/_/g;
-      $new.= "[$ori]" if $o{a};
-      $tags{$ori} = $new;
-      $tree =~ s/\[$ori\]/$new/;
-      # Isolate node
-      $t = substr $tree, 0, index($tree, $new);
-      my $i=length($t)-2;
-      for(my $c=1 ; $i and $c; $i--){
-         my $char = substr $t, $i, 1;
-	 $c++ if $char eq ')';
-	 $c-- if $char eq '(';
-      }
-      $t = substr $t, $i;
-      # Get children
-      $t =~ s/:[\d\.]+|[\(\)]/,/g;
-      $t =~ s/,+/,/g;
-      my $chn=0;
-      for my $child (split /,/, $t){
-         next unless $child;
-	 $child =~ s/.*\[(.+?)\]/$1/;
-	 $tags{$child} = $new;
-	 $chn++;
-      }
-      print STDERR "  Collapsing $new: $chn children.\n" unless $o{q};
-      print COLL "$new\n";
-   }
-   close LIST;
-   close COLL;
-}
-
-# Save tree
-open OUTTREE, ">", $outTree or die "Cannot create file: $outTree: $!\n";
-print OUTTREE $tree;
-close OUTTREE;
-
-# Count reads
-my %samples = ();
-my %nodes   = ();
-print STDERR "o Counting reads.\n";
-my $s = defined $o{s} ? $o{s} : "";
-open INCLASS, "<", $inClass or die "Cannot read file: $inClass: $!\n";
-while(<INCLASS>){
-   my @ln = split /\s+/;
-   $ln[0] =~ s/$s.+$//; # Sample name
-   ($samples{$ln[0]} ||= 0)++;
-   $tags{$ln[1]} ||= "[".$ln[1]."]"; # Node name
-   (($nodes{$tags{$ln[1]}} ||= {})->{$ln[0]} ||= 0)++;
-}
-close INCLASS;
-
-
-my $labs = 'LABELS';
-my $cols = 'COLORS';
-my @samples = $o{m} ? (split /,/, $o{m}) : (keys %samples);
-my @normfac = ();
-for my $sample (@samples){
-   my $col = shift @{$o{c}};
-   unless(defined $col and length($col)==6){
-      $col = '';
-      for (1 .. 3){
-	 my $v = int rand 16;
-	 $v = chr $v+55 if $v>9;
-	 $col.="$v$v";
-      }
-   }
-   my $nf = shift @{$o{N}};
-   $nf = 1 unless defined $nf and $nf>0;
-   $labs.= ','.($sample || 'unknown');
-   $cols.= ',#'.$col;
-   push @normfac, $nf+0;
-}
-
-open OUTCLASS, ">", $outClass or die "Cannot create file: $outClass: $!\n";
-print OUTCLASS "$labs\n$cols\n";
-my $tiny=0;
-for my $node (keys %nodes){
-   my $i=0;
-   for my $s (@samples){
-      $nodes{$node}->{$s} = ($nodes{$node}->{$s} || 0)/($o{T} ? ($samples{$s}||1)/(max(values %samples)*100) : ($normfac[$i++]||1));
-   }
-   my $r = round(sum(values %{$nodes{$node}}));
-   print OUTCLASS "$node,R$r";
-   for my $sample (@samples){
-      print OUTCLASS ",".round($nodes{$node}->{$sample} || 0);
-   }
-   print OUTCLASS "\n";
-   $tiny++ unless $r;
-}
-close OUTCLASS;
-
-unless($o{q}) {
-   print "Total counts per dataset:\n";
-   print "  $_\t".($samples{$_}||0)."\n" for @samples;
-}
-warn "$tiny node assignments are too small to represent. Decrease the values of -N or use an alternative like -T." if $tiny;
-

data/utils/enveomics/Scripts/RecPlot2.compareIdentities.R

@@ -1,32 +0,0 @@
-#!/usr/bin/env Rscript
-#
-# @author  Luis M. Rodriguez-R
-# @update  Jan-04-2016
-# @license artistic license 2.0
-#
-
-#= Load stuff
-args <- commandArgs(trailingOnly = F)  
-enveomics_R <- file.path(dirname(
-   sub("^--file=", "", args[grep("^--file=", args)])),
-   "lib", "enveomics.R")
-library(methods)
-source(file.path(enveomics_R, "R", "cliopts.R"))
-source(file.path(enveomics_R, "R", "recplot2.R"))
-
-#= Generate interface
-opt <- enve.cliopts(enve.recplot2.compareIdentities,
-   file.path(enveomics_R, "man", "enve.recplot2.compareIdentities.Rd"),
-   positional_arguments=2,
-   usage="usage: %prog [options] recplot-A.Rdata recplot-B.Rdata",
-   number=c("pseudocounts", "max.deviation"), ignore=c("x", "y"),
-   p_desc="Calculates the difference between identity distributions of two recruitment plots.")
-
-#= Run it!
-load(opt$args[1])
-opt$options[['x']] <- rp
-load(opt$args[2])
-opt$options[['y']] <- rp
-dist <- do.call("enve.recplot2.compareIdentities", opt$options)
-cat(dist, '\n')
-

data/utils/enveomics/Scripts/RefSeq.download.bash

@@ -1,48 +0,0 @@
-#!/bin/bash
-
-#
-# @author  Luis M. Rodriguez-R
-# @update  Oct-20-2015
-# @license artistic license 2.0
-#
-
-FTP="ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria"
-ORG=$1
-EXT=${2:-.*.gz}
-STT=${3:-Any}
-DIR=${4:-$ORG}
-
-if [[ "$ORG" == "" ]] ; then
-echo "
-Downloads a collection of sequences and/or annotations from NCBI's RefSeq.
-
-Usage:
-$0 <organism> [<extension>[ <level>[ <dir>]]]
-
-<organism>	The organism to download (e.g., Streptococcus_pneumoniae).
-<extension>	Extension to download.  Common extensions include '.fna.gz'
-		(genomic sequences), '.faa.gz' (protein sequences), and
-		'.gff.gz' (annotations).  By default: '.*.gz' (all data).
-<level>		Use only genomes with this assembly level. Common levels are
-		'Complete Genome' and 'Contig'.  By default, any assembly
-		level is allowed ('Any').
-<dir>		Directory where the files are to be downladed. By default,
-		same as <organism>.
-" >&2
-exit
-fi
-
-[[ -d "$DIR" ]] || mkdir "$DIR"
-
-curl -s "$FTP/$ORG/assembly_summary.txt" -o "$DIR/assembly_summary.txt"
-for path in $(cat "$DIR/assembly_summary.txt" \
-      | awk -F"\t" "\$12==\"$STT\" || \"$STT\"==\"Any\" {print \$20}" ) ; do
-   dir="$DIR/$(basename "$path")"
-   [[ -d "$dir" ]] || mkdir "$dir"
-   for file in $(curl -s "$path/" | awk '{print $9}') ; do
-      if [[ "$file" == *$EXT ]] ; then
-	 curl -s "$path/$file" -o "$dir/$file"
-      fi
-   done
-done
-

data/utils/enveomics/Scripts/SRA.download.bash

@@ -1,57 +0,0 @@
-#!/bin/bash
-
-#
-# @author  Luis M. Rodriguez-R
-# @license artistic license 2.0
-#
-
-DATA_LINK="https://www.ebi.ac.uk/ena/data/warehouse/filereport"
-DATA_OPS="result=read_run&fields=run_accession,fastq_ftp,fastq_md5"
-SRX=$1
-DIR=${2:-$SRX}
-
-if [[ "$SRX" == "" ]] ; then
-echo "
-Downloads the set of runs from a project, sample, or experiment in SRA.
-
-Usage:
-$0 <SRA-ID>[ <dir>]
-
-<SRA-ID>	ID of the SRA Project, Sample, or Experiment.
-<dir>		Directory where the files are to be downladed. By default,
-		same as <SRA-ID>.
-" >&2
-exit
-fi
-
-[[ -d "$DIR" ]] || mkdir "$DIR"
-
-function md5value {
-  local file=$1
-  o=$(md5 "$file" | perl -pe 's/.* //')
-  [[ -n $o ]] || o=$(md5sum-lite "$file" | awk '{print $1}')
-  [[ -n $o ]] || o=$(md5sum "$file" | awk '{print $1}')
-  echo "$o"
-}
-
-curl -s "$DATA_LINK?$DATA_OPS&accession=$SRX" -o "$DIR/srr_list.txt"
-tail -n +2 "$DIR/srr_list.txt" | while read ln ; do
-  srr=$(echo "$ln"|cut -f 1)
-  ftp=$(echo "$ln"|cut -f 2)
-  md5=$(echo "$ln"|cut -f 3)
-  dir="$DIR/$srr"
-  [[ -d "$dir" ]] || mkdir "$dir"
-  echo "o $srr" >&2
-  for uri in $(echo "$ftp" | tr ";" " ") ; do
-    file="$dir/$(basename $uri)"
-    curl "$uri" -o "$file"
-    md5obs=$(md5value "$file" 2> /dev/null)
-    if [[ "$md5" == "$md5obs"* ]] ; then
-      md5=$(echo "$md5" | perl -pe 's/^[^;]+;//')
-    else
-      echo "Corrupt file: $file" >&2
-      echo "  MD5 mismatch: $md5obs not in $md5" >&2
-      exit 1;
-    fi
-  done
-done

data/utils/enveomics/Scripts/TRIBS.plot-test.R

@@ -1,36 +0,0 @@
-#!/usr/bin/env Rscript
-#
-# @author  Luis M. Rodriguez-R
-# @update  Jan-05-2016
-# @license artistic license 2.0
-#
-
-#= Load stuff
-suppressPackageStartupMessages(library(enveomics.R))
-args <- commandArgs(trailingOnly = F)  
-enveomics_R <- file.path(dirname(
-   sub("^--file=", "", args[grep("^--file=", args)])),
-   "lib", "enveomics.R")
-
-#= Generate interface
-opt <- enve.cliopts(plot.enve.TRIBStest,
-   file.path(enveomics_R, "man", "plot.enve.TRIBStest.Rd"),
-   positional_arguments=c(1,3),
-   usage="usage: %prog [options] output.pdf [width height]",
-   mandatory=c("x"),
-   vectorize=c("xlim","ylim"),
-   number=c("xlim","ylim"),
-   defaults=c(type="overlap", xlim=NA, ylim=NA))
-
-#= Run it!
-a <- new.env()
-load(opt$options[['x']], a)
-opt$options[['x']] <- get(ls(envir=a),envir=a)
-summary(opt$options[['x']])
-if(is.na(opt$options[['xlim']][1])) opt$options[['xlim']] <- NULL
-if(is.na(opt$options[['ylim']][1])) opt$options[['ylim']] <- NULL
-args = as.list(opt$args)
-for(i in 2:3) if(length(args)>=i) args[[i]] <- as.numeric(args[[i]])
-do.call("pdf", args)
-do.call("plot.enve.TRIBStest", opt$options)
-dev.off()

data/utils/enveomics/Scripts/TRIBS.test.R

@@ -1,39 +0,0 @@
-#!/usr/bin/env Rscript
-#
-# @author  Luis M. Rodriguez-R
-# @update  Jan-05-2016
-# @license artistic license 2.0
-#
-
-#= Load stuff
-suppressPackageStartupMessages(library(enveomics.R))
-args <- commandArgs(trailingOnly = F)  
-enveomics_R <- file.path(dirname(
-   sub("^--file=", "", args[grep("^--file=", args)])),
-   "lib", "enveomics.R")
-
-#= Generate interface
-opt <- suppressWarnings(enve.cliopts(enve.tribs,
-   file.path(enveomics_R, "man", "enve.tribs.Rd"),
-   positional_arguments=c(0,2),
-   usage="usage: %prog [options] [output.Rdata [bins=50]]",
-   mandatory=c("dist", "selection"),
-   defaults=c(dimensions=0, selection=NULL),
-   ignore=c("metaMDS.opts","points","pre.tribs","subsamples"),
-   o_desc=list(dist="A tab-delimited matrix of distances.",
-      selection="A list of names with the selection to evaluate."),
-   p_desc=paste("",
-      "Estimates the empirical difference between all the distances",
-      "in a set of objects and a subset, together with its statistical",
-      "significance.",sep="\n\t")))
-
-#= Run it!
-opt$options[['dist']] <- as.dist(read.table(opt$options[['dist']],
-   header=TRUE, sep="\t", row.names=1))
-opt$options[['selection']] <- read.table(opt$options[['selection']],
-   header=FALSE, sep="\t", as.is=TRUE)[,1]
-if(opt$options[['dimensions']]==0) opt$options[['dimensions']] <- NULL
-if(length(opt$args)>1) opt$options[['bins']] <- as.numeric(opt$args[2])
-t <- do.call("enve.tribs.test", opt$options)
-summary(t)
-if(length(opt$args)>0) save(t, file=opt$args[1])