miga-base 0.7.24.0 → 0.7.26.0

data/utils/enveomics/Scripts/BlastTab.recplot2.R

@@ -1,48 +0,0 @@
-#!/usr/bin/env Rscript
-
-# @author  Luis M. Rodriguez-R
-# @license Artistic-2.0
-
-#= Load stuff
-suppressPackageStartupMessages(library(enveomics.R))
-args <- commandArgs(trailingOnly = FALSE)
-enveomics_R <- file.path(dirname(
-  sub("^--file=", "", args[grep("^--file=", args)])),
-  "lib", "enveomics.R")
-
-#= Generate interface
-opt <- enve.cliopts(enve.recplot2,
-  file.path(enveomics_R, "man", "enve.recplot2.Rd"),
-  positional_arguments=c(1,4),
-  usage="usage: %prog [options] output.Rdata [output.pdf [width height]]",
-  mandatory=c("prefix"),
-  o_desc=list(pos.breaks="Breaks in the positions histogram.",
-    pos.breaks.tsv="File with (absolute) coordinates of breaks in the position histogram",
-    id.breaks="Breaks in the identity histogram.",
-    id.summary="Function summarizing the identity bins. By default: sum.",
-    peaks.col="Color of peaks, mandatory for peak-finding (e.g., darkred).",
-    peaks.method="Method to detect peaks; one of emauto, em, or mower."),
-  p_desc=paste("","Produce recruitment plot objects provided that",
-    "BlastTab.catsbj.pl has been previously executed.", sep="\n\t"),
-  ignore=c("plot"),
-  defaults=c(pos.breaks.tsv=NA, id.metric="identity", peaks.col=NA,
-    peaks.method="emauto"))
-
-#= Run it!
-if(length(opt$args)>1){
-  args = as.list(opt$args[-1])
-  for(i in 2:3) if(length(args)>=i) args[[i]] <- as.numeric(args[[i]])
-  do.call("pdf", args)
-}else{
-  opt$options[["plot"]] <- FALSE
-}
-pc <- opt$options[["peaks.col"]]
-if(!is.na(pc) && pc=="NA") opt$options[["peaks.col"]] <- NA
-if(!is.null(opt$options[["peaks.method"]])){
-  opt$options[["peaks.opts"]] <- list(method=opt$options[["peaks.method"]])
-  opt$options[["peaks.method"]] <- NULL
-}
-rp <- do.call("enve.recplot2", opt$options)
-save(rp, file=opt$args[1])
-if(length(opt$args)>1) dev.off()
-

data/utils/enveomics/Scripts/BlastTab.seqdepth.pl

@@ -1,86 +0,0 @@
-#!/usr/bin/env perl
-#
-# @author: Luis M Rodriguez-R <lmrodriguezr at gmail dot com>
-# @license: artistic license 2.0
-# @update: Mar-23-2015
-#
-
-use strict;
-use warnings;
-use List::Util qw/min max sum/;
-
-my $fna = shift @ARGV;
-$fna or die "
-Usage:
-   cat blast1... | $0 genes_or_ctgs.fna > genes_or_ctgs.cov
-
-   blast1...		One or more Tabular BLAST files of reads vs genes (or contigs).
-   genes_or_ctgs.fna	A FastA file containing the genes or the contigs (db).
-   genes_or_ctgs.cov	The output file.
-   
-Output:
-   A tab-delimited file with the following columns:
-   1. Subject ID
-   2. Average sequencing depth
-   3. Median sequencing depth
-   4. Number of mapped reads
-   5. Length of the subject sequence
-
-";
-
-my $size  = {};
-my $gene  = {};
-my $reads = {};
-
-SIZE:{
-   local $/=">";
-   print STDERR "== Reading fasta\n";
-   open FNA, "<", $fna or die "Cannot read the file: $fna: $!\n";
-   my $i=0;
-   while(<FNA>){
-      chomp;
-      my @g = split /\n/, $_, 2;
-      next unless $g[1];
-      #$g[1] =~ s/[^A-Za-z]//g;
-      #$size->{$g[0]} = length $g[1];
-      $g[0] =~ s/\s.*//;
-      $size->{$g[0]} = ( $g[1] =~ tr/[A-Za-z]// );
-      print STDERR " Measuring sequence ".($i).": $g[0]      \r" unless ++$i%500;
-   }
-   close FNA;
-   print STDERR " Found $i sequences".(" "x30)."\n";
-}
-
-MAP:{
-   print STDERR "== Reading mapping\n";
-   my $i=0;
-   while(<>){
-      my @ln = split /\t/;
-      $gene->{$ln[1]} ||= [];
-      for my $pos (min($ln[8], $ln[9]) .. max($ln[8], $ln[9])){ ($gene->{$ln[1]}->[$pos]||=0)++ }
-      ($reads->{$ln[1]} ||= 0)++;
-      print STDERR " Saving hit ".($i).": $ln[1]      \r" unless ++$i%5000;
-   }
-   print STDERR " Found $i hits".(" "x30)."\n";
-}
-
-OUT:{
-   print STDERR "== Creating output\n";
-   my $i=0;
-   for my $g (keys %$gene){
-      $gene->{$g}->[$_] ||= 0 for (0 .. $size->{$g});
-      my @sorted = sort {$a <=> $b} @{$gene->{$g}};
-      die "Cannot find gene in $fna: $g.\n" unless exists $size->{$g};
-      printf "%s\t%.6f\t%d\t%d\t%d\n", $g,
-	   sum(@{$gene->{$g}})/$size->{$g},
-	   $sorted[$#sorted/2],
-	   $reads->{$g},
-	   $size->{$g};
-      delete $gene->{$g};
-      print STDERR " Saving sequence $g:".($i)."\r" unless ++$i%500;
-   }
-   print STDERR " Saved $i sequences".(" "x30)."\n";
-}
-
-print STDERR " done.\n";
-

data/utils/enveomics/Scripts/BlastTab.seqdepth_ZIP.pl

@@ -1,119 +0,0 @@
-#!/usr/bin/env perl
-#
-# @author: Luis M Rodriguez-R <lmrodriguezr at gmail dot com>
-# @license: artistic license 2.0
-# @update: Mar-23-2015
-#
-
-use strict;
-use warnings;
-use List::Util qw/min max sum/;
-
-my $fna = shift @ARGV;
-$fna or die "
-Description:
-   Estimates the average sequencing depth of subject sequences (genes or contigs)
-   assuming a Zero-Inflated Poisson distribution (ZIP) to correct for non-covered
-   positions. It uses the corrected method of moments estimators (CMMEs) as described
-   by Beckett et al [1]. Note that [1] has a mistake in eq. (2.4), that should be:
-      pi-hat-MM = 1 - (X-bar / lambda-hat-MM)
-   
-   Also note that a more elaborated mixture distribution can arise from coverage
-   histograms (e.g., see [2] for an additional correction called 'tail distribution'
-   and mixtures involving negative binomial) so take these results cum grano salis.
-
-Usage:
-   cat blast1... | $0 genes_or_ctgs.fna > genes_or_ctgs.cov
-
-   blast1...		One or more Tabular BLAST files of reads vs genes (or contigs).
-   genes_or_ctgs.fna	A FastA file containing the genes or the contigs (db).
-   genes_or_ctgs.cov	The output file.
-   
-Output:
-   A tab-delimited file with the following columns (the one you want is #2):
-   1. Subject ID
-   2. Estimated average sequencing depth (CMME lambda)
-   3. Zero-inflation (CMME pi)
-   4. Observed average sequencing depth
-   5. Observed median sequencing depth
-   6. Observed median sequencing depth excluding zeroes
-   7. Number of mapped reads
-   8. Length of the subject sequence
-
-References:
-   [1] http://anisette.ucs.louisiana.edu/Academic/Sciences/MATH/stage/stat2012.pdf
-   [2] Lindner et al, Bioinformatics, 2013.
-
-";
-
-my $size  = {};
-my $gene  = {};
-my $reads = {};
-
-SIZE:{
-   local $/=">";
-   print STDERR "== Reading fasta\n";
-   open FNA, "<", $fna or die "Cannot read the file: $fna: $!\n";
-   my $i=0;
-   while(<FNA>){
-      chomp;
-      my @g = split /\n/, $_, 2;
-      next unless $g[1];
-      #$g[1] =~ s/[^A-Za-z]//g;
-      #$size->{$g[0]} = length $g[1];
-      $g[0] =~ s/\s.*//;
-      $size->{$g[0]} = ( $g[1] =~ tr/[A-Za-z]// );
-      print STDERR " Measuring sequence ".($i).": $g[0]      \r" unless ++$i%500;
-   }
-   close FNA;
-   print STDERR " Found $i sequences".(" "x30)."\n";
-}
-
-MAP:{
-   print STDERR "== Reading mapping\n";
-   my $i=0;
-   while(<>){
-      my @ln = split /\t/;
-      $gene->{$ln[1]} ||= [];
-      for my $pos (min($ln[8], $ln[9]) .. max($ln[8], $ln[9])){ ($gene->{$ln[1]}->[$pos]||=0)++ }
-      ($reads->{$ln[1]} ||= 0)++;
-      print STDERR " Saving hit ".($i).": $ln[1]      \r" unless ++$i%5000;
-   }
-   print STDERR " Found $i hits".(" "x30)."\n";
-}
-
-OUT:{
-   print STDERR "== Creating output\n";
-   my $i=0;
-   for my $g (keys %$gene){
-      unless(exists $size->{$g}){
-         warn "Warning: Cannot find gene in $fna: $g.\n";
-	 next;
-      }
-      $gene->{$g}->[$_] ||= 0 for (0 .. $size->{$g});
-      die "Hits out-of-boundaries in gene $g: $#{$gene->{$g}} != $size->{$g}.\n" if $#{$gene->{$g}} != $size->{$g};
-      my @sorted = sort {$a <=> $b} @{$gene->{$g}};
-      my @sorted_nz = grep { $_>0 } @sorted;
-      my $xbar = sum(@{$gene->{$g}})/$size->{$g};
-      my $xsqbar = sum(map { ($_ - $xbar)**2 } @{$gene->{$g}})/($size->{$g}-1); 
-      my $var = $xsqbar - $xbar**2;
-      my $lambdaMM = $xbar + ($var/$xbar) - 1;
-      my $piMM = $lambdaMM==0 ? 0 : 1 - $xbar/$lambdaMM;
-      printf "%s\t%.6f\t%.6f\t%.6f\t%d\t%d\t%d\t%d\n", $g,
-	   ($xbar >= $var ? $xbar : $lambdaMM),
-	   ($xbar >= $var ? 0 : $piMM),
-	   #$lambdaMM,
-	   #$piMM,
-	   sum(@{$gene->{$g}})/$size->{$g},
-	   $sorted[$#sorted/2],
-	   $sorted_nz[$#sorted_nz/2],
-	   $reads->{$g},
-	   $size->{$g};
-      delete $gene->{$g};
-      print STDERR " Saving sequence $g:".($i)."   \r" unless ++$i%500;
-   }
-   print STDERR " Saved $i sequences".(" "x30)."   \n";
-}
-
-print STDERR " done.\n";
-

data/utils/enveomics/Scripts/BlastTab.seqdepth_nomedian.pl

@@ -1,86 +0,0 @@
-#!/usr/bin/env perl
-#
-# @author: Luis M Rodriguez-R <lmrodriguezr at gmail dot com>
-# @license: artistic license 2.0
-# @update: Mar-23-2015
-#
-
-use strict;
-use warnings;
-use List::Util qw/min max sum/;
-
-my $fna = shift @ARGV;
-$fna or die "
-Usage:
-   cat blast1... | $0 genes_or_ctgs.fna > genes_or_ctgs.cov
-
-   blast1...		One or more Tabular BLAST files of reads vs genes (or contigs).
-   genes_or_ctgs.fna	A FastA file containing the genes or the contigs (db).
-   genes_or_ctgs.cov	The output file.
-
-Output:
-   A tab-delimited file with the following columns:
-   1. Subject ID
-   2. Average sequencing depth
-   3. Number of mapped reads
-   4. Length of the subject sequence
-
-Note:
-   The values reported by this script may differ from those of BlastTab.seqdepth.pl,
-   because this script uses the aligned length of the read while BlastTab.seqdepth.pl
-   uses the aligned length of the subject sequence. 
-
-";
-
-my $size  = {};
-my $gene  = {};
-my $reads = {};
-
-SIZE:{
-   local $/=">";
-   print STDERR "== Reading fasta\n";
-   open FNA, "<", $fna or die "Cannot read the file: $fna: $!\n";
-   my $i=0;
-   while(<FNA>){
-      chomp;
-      my @g = split /\n/, $_, 2;
-      next unless $g[1];
-      #$g[1] =~ s/[^A-Za-z]//g;
-      #$size->{$g[0]} = length $g[1];
-      $g[0] =~ s/\s.*//;
-      $size->{$g[0]} = ( $g[1] =~ tr/[A-Za-z]// );
-      print STDERR " Measuring sequence ".($i).": $g[0]      \r" unless ++$i%500;
-   }
-   close FNA;
-   print STDERR " Found $i sequences".(" "x30)."\n";
-}
-
-MAP:{
-   print STDERR "== Reading mapping\n";
-   my $i=0;
-   while(<>){
-      my @ln = split /\t/;
-      $gene->{$ln[1]} ||= 0;
-      $gene->{$ln[1]} += abs($ln[6]-$ln[7])+1;
-      ($reads->{$ln[1]} ||= 0)++;
-      print STDERR " Saving hit ".($i).": $ln[1]      \r" unless ++$i%5000;
-   }
-   print STDERR " Found $i hits".(" "x30)."\n";
-}
-
-OUT:{
-   print STDERR "== Creating output\n";
-   my $i=0;
-   for my $g (keys %$gene){
-      die "Cannot find gene in $fna: $g.\n" unless exists $size->{$g};
-      printf "%s\t%.6f\t%d\t%d\n", $g,
-	   $gene->{$g}/$size->{$g},
-	   $reads->{$g},
-	   $size->{$g};
-      print STDERR " Saving sequence $g:".($i)."\r" unless ++$i%500;
-   }
-   print STDERR " Saved $i sequences".(" "x30)."\n";
-}
-
-print STDERR " done.\n";
-

data/utils/enveomics/Scripts/BlastTab.subsample.pl

@@ -1,47 +0,0 @@
-#!/usr/bin/env perl
-#
-# @author  Luis M Rodriguez-R <lmrodriguezr at gmail dot com>
-# @license artistic license 2.0
-# @update  Mar-23-2015
-#
-
-use strict;
-use warnings;
-
-my($blast, $fasta) = @ARGV;
-($blast and $fasta) or die "
-Description:
-   Filters a BLAST output including only the hits produced by
-   any of the given sequences as query.
-
-Usage:
-   $0 blast.tab sample.fa > out.tab
-
-   blast.tab	BLAST output to be filtered (tabular format).
-   sample.fa	Sequences to use as query.
-   out.tab	The filtered BLAST output (tabular format).
-
-";
-
-print STDERR "== Reading sequences\n";
-my $seq = {};
-open FASTA, "<", $fasta or die "Cannot read the file: $fasta: $!\n";
-while(<FASTA>){
-   next unless /^>(\S+)/;
-   $seq->{$1} = 1;
-}
-close FASTA;
-print STDERR " ".(scalar keys %$seq)." sequences to be used as query.\n";
-
-print STDERR "== Reading BLAST\n";
-my ($N,$n)=(0,0);
-open BLAST, "<", $blast or die "Cannot read the file: $blast: $!\n";
-while(my $ln = <BLAST>){
-   next if $ln=~/^#/;
-   $N++; my ($qry) = split /\t/, $ln;
-   next unless exists $seq->{$qry};
-   $n++; print $ln;
-}
-close BLAST;
-print STDERR " Reported $n entries out of $N.\n";
-

data/utils/enveomics/Scripts/BlastTab.sumPerHit.pl

@@ -1,114 +0,0 @@
-#!/usr/bin/env perl
-#
-# @author  Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>
-# @update  Mar-23-2016
-# @license artistic license 2.0
-#
-
-use warnings;
-use strict;
-use Getopt::Std;
-
-sub HELP_MESSAGE {
-die "
-.Description
-   Sums the weights of all the queries hitting each subject.  Often (but not
-   necessarily) the BLAST files contain only best matches.  The weights can be
-   any number, but a common use of this Script is to add up counts (weights are
-   integers).  For example, in a BLAST of predicted genes vs some annotation
-   source, the weights could be the number of reads recruited by each gene.
-
-.Usage:
-   $0 [options] blast... > out-file
-
-   blast... *	One or more BLAST files.
-   out-file	A two-columns tab-delimited file containing the summed weights
-   		per hit.
-   
-   -w <str>	Weights file: A two-columns tab-delimited file containing the
-   		name (column 1) and the weight (column 2) of each query.
-   -s <float>	Minimum score.  By default: 0.
-   -i <float>	Minimum identity (in percentage).  By default: 0.
-   -m <int>	Maximum number of queries.  Set to 0 for all.  By default: 0.
-   -n		Normalize weights by the number of hits per query.
-   -z		Add zero when weight is not found (by default: doesn't list
-   		them).
-   -q		Run quietly.
-   -h		Display this message and exit.
-
-   * Mandatory
-
-.Note:
-   The weights (-w parameter) are optional, but its use is encouraged.  When
-   weights are not passed, the script simply assumes all queries to be equally
-   weighted (unity), a result that can be faster to compute with, for example:
-      cat blast | cut -f 2 | sort | uniq -c | awk '{print \$2\"\\t\"\$1}' > out
-   It is equivalent to simply count the number of times that each subject
-   occurs.
-"
-}
-
-my %o = ();
-getopts('w:s:i:m:znqh', \%o);
-$o{h} and &HELP_MESSAGE;
-$o{s}||=0;
-$o{i}||=0;
-$o{m}||=0;
-
-my %count;
-if($o{w}){
-   print STDERR "Reading counts.\n" unless $o{q};
-   open COUNT, "<", $o{w} or die "Cannot open file: $o{w}: $!\n";
-   %count = map {split /\t/} <COUNT>;
-   close COUNT;
-}
-
-print STDERR "Reading BLASTs.\n" unless $o{q};
-my $qry = '';
-my $hits = 0;
-my @buf = ();
-my $qries = 0;
-my $noQry = 0;
-my $ln1   = 0;
-my %out = ();
-BFILE: for my $blast (@ARGV){
-   print STDERR " o $blast\n" unless $o{q};
-   open BLAST, "<", $blast or die "Cannot open file: $blast: $!\n";
-   BLINE: while(<BLAST>){
-      chomp;
-      my @ln = split /\t/;
-      $ln1 ||= $#ln;
-      die "Bad line $.: $_\n" unless $#ln==$ln1;
-      next if ($o{s} and $ln[11]<$o{s}) or ($o{i} and $ln[2]<$o{i});
-      unless(exists $count{$ln[0]}){
-	 $noQry++;
-	 if(not $o{w}){
-	    $count{$ln[0]}=1;
-	 }elsif($o{z}){
-	    $count{$ln[0]}=0;
-	 }else{
-	    next BLINE;
-	 }
-      }
-      
-      if($qry ne $ln[0]){
-	 $qries++;
-	 ($out{$_->[0]}||=0) += ($_->[1]/($o{n}?$hits:1)) for @buf;
-	 last BFILE if $o{m} and $qries >= $o{m};
-	 @buf = ();
-	 $qry  = $ln[0];
-	 $hits = 0;
-      }
-      
-      push @buf, [$ln[1], $count{$ln[0]}];
-      $hits++;
-   }
-   ($out{$_->[0]}||=0) += ($_->[1]/($o{n}?$hits:1)) for @buf;
-   close BLAST;
-}
-print STDERR "Warning: Couldn't find $noQry queries\n" if $noQry and $o{w};
-
-for my $h (keys %out){
-   print "$h\t".$out{$h}."\n";
-}
-