miga-base 1.2.15.1 → 1.2.15.3

data/utils/enveomics/Scripts/FastA.qlen.pl

@@ -1,57 +0,0 @@
-#!/usr/bin/env perl
-#
-# @author  Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>
-# @update  Dec-22-2015
-# @license artistic license 2.0
-#
-use strict;
-use warnings;
-use List::Util qw/sum min max/;
-
-my ($seqs, $minlen) = @ARGV;
-$seqs or die "
-Description:
-   Calculates the quartiles of the length in a set of sequences.  The Q2 is
-   also known as the median.  Q0 is the minimum length, and Q4 is the maximum
-   length.  It also calculates TOTAL, the added length of the sequences in
-   the file, and AVG, the average length.
-   
-Usage:
-   $0 seqs.fa[ minlen]
-
-   seqs.fa	A FastA file containing the sequences.
-   minlen	(optional) The minimum length to take into consideration.
-   		By default: 0.
-
-";
-$minlen ||= 0;
-
-# Read files
-my @len = ();
-open FA, "<", $seqs or die "Cannot open file: $seqs: $!\n";
-my $def = '';
-my $len = 0;
-while(<FA>){
-   next if /^;/;
-   if(m/^>(\S+)\s?/){
-      push(@len, int($len)) if $def and not $len<$minlen;
-      $def = $1;
-      $len = 0;
-   }else{
-      s/[^A-Za-z]//g;
-      $len+= length $_;
-   }
-}
-push(@len, int($len)) if $def and not $len<$minlen;
-close FA;
-
-# Sort and estimates quantiles
-@len = sort { $a <=> $b } @len;
-for my $q (0 .. 4){
-   my $ii = int(my $i = $#len*$q/4);
-   print "Q$q: ".($i==$ii ? $len[$i] : ($len[$ii]+$len[$ii+1])/2 )."\n";
-}
-my $sum = sum @len;
-print "N: ".scalar(@len)."\n";
-print "TOTAL: $sum\n";
-print "AVG: ".($sum/scalar(@len))."\n";

data/utils/enveomics/Scripts/FastA.rename.pl

@@ -1,65 +0,0 @@
-#!/usr/bin/env perl
-#
-# @author  Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>
-# @update  Oct-07-2015
-# @license artistic license 2.0
-#
-
-use warnings;
-use strict;
-use Getopt::Std;
-
-sub HELP_MESSAGE { die "
-.Description:
-   Renames a set of sequences in FastA format.
-
-.Usage: $0 [options] list.txt seqs.fa > renamed.fa
-   
-   [options]
-   -f		Filter list.  Ignores sequences NOT present in the list.
-   -q		Runs quietly.
-   -h		Prints this message and exits.
-
-   [mandatory]
-   list.txt	Tab-delimited list of sequences, with the original ID in the
-   		first column and the ID to use in the second.
-   seqs.fa	FastA file containing the superset of sequences.
-   renamed.fa	FastA file to be created.
-
-" }
-
-my %o=();
-getopts('fhq', \%o);
-my($list, $fa) = @ARGV;
-($list and $fa) or &HELP_MESSAGE;
-$o{h} and &HELP_MESSAGE;
-
-print STDERR "Reading list.\n" unless $o{q};
-open LI, "<", $list or die "Cannot read file: $list: $!\n";
-my %li = map { my $l=$_; chomp $l; my @r=split(/\t/,$l); $r[0] => $r[1] } <LI>;
-close LI;
-
-print STDERR "Renaming FastA.\n" unless $o{q};
-open FA, "<", $fa or die "Cannot read file: $fa: $!\n";
-my $good = 0;
-while(my $ln = <FA>){
-   next if $ln =~ /^;/;
-   chomp $ln;
-   if($ln =~ m/^>((\S+).*)/){
-      my $rep=0;
-      $rep = ">".$li{$ln} if exists $li{$ln};
-      $rep = ">".$li{$1} if exists $li{$1} and not $rep;
-      $rep = ">".$li{">$1"} if exists $li{">$1"} and not $rep;
-      $rep = ">".$li{$2} if exists $li{$2} and not $rep;
-      if($rep){
-	 $ln = $rep;
-	 $good = 1;
-      }
-   }elsif($ln =~ m/^>/){
-      $good=0;
-      print STDERR "Warning: Non-cannonical defline, line $.: $ln\n";
-   }
-   print "$ln\n" if $good or not $o{f};
-}
-close FA;
-

data/utils/enveomics/Scripts/FastA.revcom.pl

@@ -1,23 +0,0 @@
-#!/usr/bin/env perl
-#
-# @author: Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>
-# @update: Dec-25-2015
-# @license: artistic license 2.0
-#
-use strict;
-use warnings;
-use Bio::SeqIO;
-
-($ARGV[0] and $ARGV[0] =~ /--?h(elp)?/) and die "
-Description:
-   Reverse-complement sequences in FastA format.
-
-Usage:
-   $0 < input.fa > output.fa
-
-";
-
-my @len = ();
-my $seqI = Bio::SeqIO->new(-fh => \*STDIN, -format=>"FastA");
-my $seqO = Bio::SeqIO->new(-fh => \*STDOUT, -format=>"FastA");
-while(my $seq = $seqI->next_seq){ $seqO->write_seq($seq->revcom) }

data/utils/enveomics/Scripts/FastA.sample.rb

@@ -1,98 +0,0 @@
-#!/usr/bin/env ruby
-
-# frozen_string_literal: false
-
-$VERSION = 1.0
-$:.push File.expand_path('../lib', __FILE__)
-require 'enveomics_rb/enveomics'
-
-o = { q: false, rep: false }
-
-OptionParser.new do |opt|
-  Enveomics.opt_banner(
-    opt, 'Samples a random set of sequences from a multi-FastA file',
-    "#{File.basename($0)} -i seq.fa -o 10pc.fa -f 0.1 [options]"
-  )
-  opt.separator 'Mandatory'
-  opt.on(
-    '-i', '--in PATH',
-    'Input FastA file',
-    'Supports compression with .gz extension, use - for STDIN'
-  ) { |v| o[:i] = v }
-  opt.on(
-    '-o', '--out PATH',
-    'Output FastA file',
-    'Supports compression with .gz extension, use - for STDOUT'
-  ) { |v| o[:o] = v }
-  opt.on(
-    '-f', '--fraction FLOAT', Float,
-    'Fraction of sequences to sample [0-1].',
-    'Mandatory unless -c is provided.'
-  ) { |v| o[:f] = v }
-  opt.separator ''
-
-  opt.separator 'Options'
-  opt.on(
-    '-c', '--number INT', Integer,
-    'Number of sequences to sample',
-    'Mandatory unless -f is provided'
-  ) { |v| o[:n] = v }
-  opt.on('-r', '--replacement','Sample with replacement') { |v| o[:rep] = v }
-  opt.on('-q', '--quiet', 'Run quietly (no STDERR output)') { o[:q] = true }
-  opt.on('-h', '--help', 'Display this screen.') do
-    puts opt
-    exit
-  end
-  opt.separator ''
-end.parse!
-
-raise Enveomics::OptionError.new('-i is mandatory') if o[:i].nil?
-raise Enveomics::OptionError.new('-o is mandatory') if o[:o].nil?
-if o[:f].nil? && o[:n].nil?
-  raise Enveomics::OptionError.new('-f or -n is mandatory')
-end
-$QUIET = o[:q]
-
-# Functions to parse sequences
-def do_stuff(id, sq)
-  return if id.nil? or sq.empty?
-  @n_in += 1
-  sq.gsub!(/[^A-Za-z]/, '')
-  i = 0
-  @coll.extract(id, sq).each do |new_sq|
-    @ofh.puts ">#{id}:#{i += 1}"
-    @ofh.puts new_sq
-    @n_out += 1
-  end
-end
-
-# Parse sequences
-say 'Parsing sequences'
-seq = []
-fh = reader(o[:i])
-id = nil
-sq = ''
-fh.each do |ln|
-  next if ln =~ /^;/
-  if ln =~ /^>(.+)/
-    seq << [id, sq] unless id.nil?
-    id = $1
-    sq = ''
-  else
-    sq << ln
-  end
-end
-seq << [id, sq] unless id.nil?
-fh.close
-say "Input sequences: #{seq.size}"
-
-o[:n] ||= (seq.size * o[:f]).round
-seq_o = o[:rep] ? o[:n].times.map { seq.sample } : seq.sample(o[:n])
-fh = writer(o[:o])
-seq_o.each do |i|
-  fh.puts ">#{i[0]}"
-  fh.puts i[1]
-end
-fh.close
-say "Output sequences: #{seq_o.size}"
-

data/utils/enveomics/Scripts/FastA.slider.pl

@@ -1,85 +0,0 @@
-#!/usr/bin/env perl
-#
-# @author  Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>
-# @update  Oct-07-2015
-# @license artistic license 2.0
-# 
-
-use strict;
-use List::Util qw/min/;
-
-push @ARGV, undef unless $#ARGV%2;
-my %params = @ARGV;
-
-die "
-Usage:
-   $0 [options] < in.fa > out.fa
-
-   in.fa	Input file in FastA format.
-   out.fa	Output file in FastA format.
-
-Options:
-   -seq <str>	Input file.  If not set, it is expected to be in STDIN.
-   -out <str>	Output file.  If not set, it is sent to STDOUT.
-   -win <int>	Window size.  By default: 18.
-   -step <int>	Step size.  By default: 1.
-   -lerr <int>	Expected error in chunks length.  By default: 2.
-   -comm <1|0>	Generate FastA comments (leaded by semi-colon) to separate
-		input sequences.  By default: 0.
-   -short <1|0>	Use chunks shorter than the window size 'as is'. By
-		default: 0 (discard those chunks).
-   -h		Displays this help message and exits.
-
-" if exists $params{'--help'} or
-   exists $params{'-h'} or exists $params{'-help'};
-
-if($params{'-seq'}){
-   open SEQ, "<", $params{'-seq'} or
-      die "I can not open '".$params{'-seq'}."': $!\n";
-}else{
-   *SEQ = *STDIN;
-   print STDERR "Please input your sequence, and hit ".
-      "Intro and Ctrl+D when you are done:\n";
-}
-
-if($params{'-out'}){
-   open OUT, ">", $params{'-out'} or
-      die "I can not open '".$params{'-out'}."': $!\n";
-}else{
-   *OUT = *STDOUT;
-}
-
-$params{'-win'} ||= 18;
-$params{'-step'} ||= 1;
-$params{'-lerr'} ||= 2;
-$params{'-comm'} ||= 0;
-$params{'-short'} ||= 0;
-
-my $win = $params{'-win'}+0;
-my $stp = $params{'-step'}+0;
-my $lerr = $params{'-lerr'}+0;
-my $buffer = "";
-my $i = 0;
-while(<SEQ>){
-   next if /^;/;
-   chomp;
-   if(m/^>/){
-      print OUT ">", ++$i, "\n", $buffer, "\n" if
-	 $params{'-short'}==1 and $buffer;
-      $buffer = "";
-      print OUT ";--- INPUT: $_ ---\n" unless $params{'-comm'}==0;
-      next;
-   }
-   s/[^A-Za-z]//g;
-   $buffer.= $_;
-   while(length($buffer) >= $win){
-      print OUT ">", ++$i, "\n",
-	 substr($buffer, 0, $win+int(rand($lerr*2)-$lerr)), "\n";
-      $buffer = substr $buffer, $stp;
-   }
-}
-close SEQ if $params{'-seq'};
-close OUT if $params{'-out'};
-print STDERR "$i chunks produced.\n";
-
-

data/utils/enveomics/Scripts/FastA.split.pl

@@ -1,55 +0,0 @@
-#!/usr/bin/env perl
-#
-# @author Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>
-# @update Oct-13-2015
-# @license artistic license 2.0
-#
-
-use warnings;
-use strict;
-use Symbol;
-
-my ($file, $base, $outN) = @ARGV;
-
-$outN ||= 12;
-($file and $base) or die "
-Usage
-   $0 in_file.fa out_base[ no_files]
-   
-   in_file.fa	Input file in FastA format.
-   out_base	Prefix for the name of the output files.  It will
-   		be appended with .<i>.fa, where <i> is a consecutive
-		number starting in 1.
-   no_files	Number of files to generate.  By default: 12.
-
-";
-
-
-my @outSym = ();
-for my $i (1 .. $outN){
-   $outSym[$i-1] = gensym;
-   open $outSym[$i-1], ">", "$base.$i.fa" or
-      die "I can not create the file: $base.$i.fa: $!\n";
-}
-
-
-my($i, $seq) = (-1, '');
-open FILE, "<", $file or die "I can not read the file: $file: $!\n";
-while(my $ln=<FILE>){
-   next if $ln=~/^;/;
-   if($ln =~ m/^>/){
-      print { $outSym[$i % $outN] } $seq if $seq;
-      $i++;
-      $seq = '';
-   }
-   $seq.=$ln;
-}
-print { $outSym[$i % $outN] } $seq if $seq;
-close FILE;
-
-for(my $j=0; $j<$outN; $j++){
-   close $outSym[$j];
-}
-
-print STDERR "Sequences: ".($i+1)."\nFiles: $outN\n";
-

data/utils/enveomics/Scripts/FastA.split.rb

@@ -1,79 +0,0 @@
-#!/usr/bin/env ruby
-#
-# @author Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>
-# @license Artistic-2.0
-#
-
-require "optparse"
-
-o = {q:false, n:12, lett:false, dc:false, z:false, out:"%s.%s.fa"}
-ARGV << "-h" if ARGV.size==0
-
-OptionParser.new do |opt|
-  opt.banner = "
-  Evenly splits a multi-FastA file into multiple multi-FastA files.
-  
-  Usage: #{$0} [options]"
-  opt.separator ""
-  opt.separator "Mandatory"
-  opt.on("-i", "--input PATH", "Input FastA file."){ |v| o[:i] = v}
-  opt.on("-p", "--prefix PATH", "Prefix of output FastA files."){ |v| o[:p] = v}
-  opt.separator ""
-  opt.separator "Options"
-  opt.on("-n", "--number INT",
-    "Number of output files to produce. By default: #{o[:n]}."
-    ){ |v| o[:n] = v.to_i }
-  opt.on("-z", "--zero-padded",
-    "Use zero-padded numbers as output index."){ o[:lett]=false; o[:z]=true }
-  opt.on("-l", "--lowercase-letters",
-    "Use lowercase letters as output index."){ o[:lett]=true ; o[:dc]=true }
-    opt.on("-u", "--uppercase-letters",
-    "Use uppercase letters as output index."){ o[:lett]=true }
-  opt.on("-o", "--out STR",
-    "Format of output filenames, where %s are replaced by prefix and index.",
-    "By default: #{o[:out]}."){ |v| o[:out] = v }
-  opt.on("-q", "--quiet", "Run quietly (no STDERR output)."){ o[:q] = TRUE }
-  opt.on("-h", "--help", "Display this screen.") do
-    puts opt
-    exit
-  end
-  opt.separator ""
-end.parse!
-abort "-i is mandatory." if o[:i].nil?
-abort "-p is mandatory." if o[:p].nil?
-
-ofh = []
-idx = if o[:lett]
-  k = Math::log(o[:n], 26).ceil
-  r = o[:dc] ? ["a","z"] : ["A","Z"]
-  ((r[0]*k) .. (r[1]*k)).first(o[:n])
-elsif o[:z]
-  k = Math::log(o[:n], 10).ceil
-  (1 .. o[:n]).map{ |i| "%0#{k}d" % i }
-else
-  (1 .. o[:n]).map{ |i| i.to_s }
-end
-idx.each do |i|
-  fn = o[:out] % [o[:p], i]
-  ofh << File.open(fn, "w")
-end
-
-i = -1
-seq = ""
-File.open(o[:i], "r") do |ifh|
-  ifh.each_line do |ln|
-    next if ln =~ /^;/
-    if ln =~ /^>/
-      ofh[i % o[:n]].print seq
-      i += 1
-      seq = ""
-    end
-    seq << ln
-  end
-  ofh[i % o[:n]].print seq
-end
-
-ofh.each{ |i| i.close }
-
-$stderr.puts "Sequences: #{i+1}.", "Files: #{o[:n]}." unless o[:q]
-

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

@@ -1,131 +0,0 @@
-#!/usr/bin/env perl
-# 
-# @author  Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>
-# @update  Oct-07-2015
-# @license artistic license 2.0
-# 
-
-use strict;
-use warnings;
-use List::Util qw| max min sum |;
-use Getopt::Std;
-use Symbol;
-
-my %o;
-getopts('f:r:o:Fzhq', \%o);
-
-my $HELP = <<HELP
-
-  Description:
-    Subsamples a set of sequences.
-
-  Usage:
-    # IMPORTANT: options *MUST* precede the input file(s).
-    $0 [options] input.fa...
-  
-  Where,
-    input.fa...	: File (or files) containing the sequences.
-  
-  Options:
-    -f <float>	: Fraction of the library to be sampled (as percentage).  It can
-    		  include several values (separated by comma), as well as ranges
-		  of values in the form 'from-to/by'.  For example, the -f value
-		  1-5/1,10-50/10,75,99 will produce 12 subsamples with expected
-		  fractions 1%, 2%, 3%, 4%, 5%, 10%, 20%, 30%, 40%, 50%, 75%,
-		  and 99%.  By default: 10.
-    -r <int>	: Number of replicates per fraction.  By default: 1.
-    -o <str>	: Prefix of the output files to be created.  The output files
-		  will have a suffix of the form '.fraction-replicate.fa', where
-		  'fraction' is the percentage sampled and 'replicate' is an
-		  increasing integer for replicates of the same fraction.  By
-		  default: Path to the input file.
-    -F		: Force overwriting output file(s).
-    -z		: Include leading zeroes in the numeric parts of the output
-    		  files (e.g., file.002.50-01.fa instead of file.2.50-1.fa), so
-		  that alphabetic sorting of files reflects the sampled
-		  fraction.
-    -q		: Run quietly.
-    -h		: Displays this message and exits.
-
-HELP
-;
-
-sub thousands($){ my $i=shift; $i=~s/(\d{1,3}?)(?=(\d{3})+$)/$1,/g; $i }
-my @in  = @ARGV;
-$o{f} ||= '10';
-$o{r} ||= 1;
-$o{o} ||= $in[0];
-$#in>=0 or die $HELP;
-
-my $samples = {};
-my $sample_no=0;
-my $format = ($o{z} ? "%s\.%08s\-%02i.fa" : "%s.%s-%s.fa");
-for my $value (split /,/, $o{f}){
-   my $from = $value;
-   my $to   = $value;
-   my $by   = 1;
-   if($value =~ m/^([^-]+)-([^\/]+)\/(.+)$/){
-      $from = $1;
-      $to   = $2;
-      $by   = $3;
-      ($from,$to) = ($to,$from) if $from > $to;
-   }
-   for(my $p=$from; $p<=$to; $p+=$by){
-      die "Percentage out of the [0,100] range: $p\n" if $p>100 or $p<0;
-      $samples->{$p} ||= [];
-      for (1 .. $o{r}){
-         my $r = $#{$samples->{$p}}+2;
-         my $file = sprintf $format, $o{o}, sprintf("%.4f", $p), $r;
-	 die "File exists: $file.\n" if !$o{F} and -e $file;
-	 $samples->{$p}->[$r-1] = [$p, 0, gensym(), $file];
-	 open $samples->{$p}->[$r-1]->[2], ">", $file;
-	 $sample_no++;
-      }
-   }
-}
-print STDERR "Open samples: $sample_no.\n" unless $o{q};
-
-my $sprob = ($o{s} || '10');
-
-die $HELP unless $sprob and $#in>=0;
-$o{'h'} and die $HELP;
-
-my $N  = 0;
-my @ck = qw(*... **.. ***. .*** ..** ...*);
-SAMPLING: {
-   local $/ = "\n>";
-   print STDERR "Sampling sequences.\n" unless $o{q};
-   FILE: for my $in (@in){
-      open IN, '<', $in or die "I can not open $in: $!\n";
-      SEQ: while(my $seq = <IN>){
-	 $N++;
-	 $seq =~ s/^>?/>/;
-	 $seq =~ s/>$//;
-	 $seq =~ s/^;.*//gm;
-	 PERC: for my $sperc (values %$samples){
-	    SAMPLE: for my $sample (@$sperc){
-	       if($sample->[0] > rand 100){
-		  $sample->[1]++;
-		  print { qualify_to_ref $sample->[2] } $seq;
-	       }
-	    }
-	 }
-	 print STDERR " [".$ck[($N/5000)%@ck]."] ".&thousands($N).
-	    " seqs.    \r" unless $o{q} or $N%5000;
-      }
-      close IN;
-   }
-}
-
-print STDERR "  Total sequences: ".&thousands($N).".    \n" unless $o{q};
-for my $p (values %$samples){
-   for my $s (@$p){
-      printf STDERR "
-      Sample file:       %s
-      Sampled sequences: %d
-      Sampled fraction:  %.2f%%\n",
-      $s->[3], $s->[1], $s->[1]*100/$N unless $o{q};
-      close $s->[2];
-   }
-}
-

data/utils/enveomics/Scripts/FastA.tag.rb

@@ -1,65 +0,0 @@
-#!/usr/bin/env ruby
-
-# @author  Luis M. Rodriguez-R
-# @license artistic license 2.0
-
-require 'optparse'
-
-o = {q: false, p: '', s: '', d: false}
-ARGV << '-h' if ARGV.size==0
-OptionParser.new do |opts|
-  opts.banner = "
-Generates easy-to-parse tagged reads from FastA files.
-
-Usage: #{$0} [options]"
-  opts.separator ''
-  opts.separator 'Mandatory'
-  opts.on('-i', '--in FILE',
-    'Path to the FastA file containing the sequences.'){ |v| o[:in] = v }
-  opts.on('-o', '--out FILE',
-    'Path to the FastA to create.'){ |v| o[:out] = v }
-  opts.separator ''
-  opts.separator 'ID options'
-  opts.on('-p', '--prefix STR', 'Prefix to use in all IDs.'){ |v| o[:p] = v }
-  opts.on('-s', '--suffix STR', 'Suffix to use in all IDs.'){ |v| o[:s] = v }
-  opts.on('-d', '--defline',
-    'Keep the original defline after a space.'){ o[:d] = true }
-  opts.on('-l', '--list FILE',
-    'Reads a list of IDS.'){ |v| o[:l] = v }
-  opts.separator ''
-  opts.separator 'Other Options'
-  opts.on('-q', '--quiet', 'Run quietly (no STDERR output)'){ o[:q] = true }
-  opts.on('-h', '--help', 'Display this screen') do
-    puts opts
-    exit
-  end
-  opts.separator ''
-end.parse!
-abort '-i is mandatory' if o[:in].nil?
-abort '-o is mandatory' if o[:out].nil?
-   
-begin
-  list = o[:l].nil? ? nil :
-    File.readlines(o[:l]).map{ |i| i.chomp.gsub(/^>/, '') }
-  ofh = File.open(o[:out], 'w')
-  i = 0
-  File.open(o[:in], 'r') do |ifh|
-    ifh.each do |ln|
-      ln.chomp!
-      next if ln =~ /^;/
-      unless /^>/.match(ln).nil?
-        i += 1
-        new_id = o[:l].nil? ? i : list.shift
-        ofh.puts ">#{o[:p]}#{new_id}#{o[:s]}#{o[:d]?" #{ln[1, ln.size-1]}":''}"
-      else
-        ofh.puts ln
-      end
-    end
-  end
-  ofh.close
-rescue => err
-  $stderr.puts "Exception: #{err}\n\n"
-  err.backtrace.each { |l| $stderr.puts l + "\n" }
-  err
-end
-