miga-base 0.7.24.0 → 0.7.26.0

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

@@ -1,42 +0,0 @@
-#!/usr/bin/env perl
-#
-# @author  Luis M Rodriguez-R
-# @update  Mar-23-2016
-# @license artistic license 2.0
-#
-
-use warnings;
-use strict;
-
-$#ARGV>=0 or die "
-Usage:
-   $0 seqs.fa... > gc.txt
-
-   seqs.fa	One or more FastA files.
-   gc.txt	A table with the G+C content of the sequences.
-
-";
-
-for my $fa (@ARGV){
-   open FA, "<", $fa or die "Cannot open file: $fa: $!\n";
-   my $def = "";
-   my $len = 0;
-   my $gc  = 0;
-   while(<FA>){
-      next if /^;/;
-      if(m/^>(\S*)/){
-         print "$def\t".($gc/$len)."\n" if $len;
-	 $def = $1;
-	 $len = 0;
-	 $gc  = 0;
-      }else{
-         s/[^ACTGactg]//g;
-	 $len += length $_;
-	 s/[^GC]//g;
-	 $gc  += length $_;
-      }
-   }
-   print "$def\t".($gc/$len)."\n" if $len;
-   close FA;
-}
-

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

@@ -1,93 +0,0 @@
-#!/usr/bin/env perl
-
-# @author Luis M. Rodriguez-R
-# @license artistic license 2.0
-
-use strict;
-use warnings;
-use Symbol;
-
-my $HELP = <<HELP
-
-  Description:
-    Interposes sequences in FastA format from two files into one output file.
-    If more than two files are provided, the script will interpose all the input
-    files.
-    Note that this script will check for the consistency of the names (assuming
-    a pair of related reads contains the same name varying only in a trailing
-    slash (/) followed by a digit.  If you want to turn this feature off just
-    set the -T option to zero.  If you want to decrease the sampling period (to
-    speed the script up) or increase it (to make it more sensitive to errors)
-    just change the -T option accordingly.
-
-  Usage:
-    $0 [-T <int> ]<output_fasta> <input_fasta_1> <input_fasta_2> [additional input files...]
-
-  Where,
-    -T <int>		: Optional.  Integer indicating the sampling period for
-    			  names evaluation (see Description above).
-			  By default: 1000.
-    output_fasta	: Output file
-    input_fasta_1	: First FastA file
-    input_fasta_2	: Second FastA file
-    ... 		: Any additional FastA files (or none)
-
-HELP
-;
-my $eval_T = 1000;
-if(exists $ARGV[0] and exists $ARGV[1] and $ARGV[0] eq '-T'){
-   $eval_T = $ARGV[1]+0;
-   shift @ARGV;
-   shift @ARGV;
-}
-my $out = shift @ARGV;
-my @in = @ARGV;
-$/ = "\n>";
-
-die $HELP unless $out and $#in >= 1;
-open OUT, ">", $out or die "Unable to write on $out: $!\n";
-print "Output file: $out\n";
-
-my @in_fh = ();
-
-for my $k (0 .. $#in) {
-   $in_fh[$k] = gensym;
-   open $in_fh[$k], "<", $in[$k] or die "Unable to read $in[$k]: $!\n";
-   print "Input file: $in[$k]\n";
-}
-
-my $i = 0;
-my $frl;
-LINE: while(1){
-   my $name = "";
-   print STDERR "\rEntry: $i    " unless $i % 1000;
-   FILE: for my $k (0 .. $#in_fh){
-      my $ln = readline($in_fh[$k]);
-      last LINE if $k==0 and not defined $ln;
-      defined $ln or die "Impossible to read next entry ($.) from $in[$k]: $!\n";
-      $ln =~ s/^\>?/>/;
-      $ln =~ s/\>$//;
-      $ln =~ s/^;.*//gm;
-      if($eval_T and not $i % $eval_T){
-	 unless($name){
-	    $ln =~ m/^>(.*?)[\/ \\_]\d+/ or die "Impossible to evaluate names!\n offending entry:\n$ln\n";
-	    $name = $1;
-	 }
-	 die "Inconsistent name!\n base name is $name\n offending entry is:\n$ln\n" unless $ln =~ /^>$name/;
-      }
-      unless($frl){
-         $ln =~ m/^>.*?\n(.*?)\n/ or die "Unexpected format!\n offending entry:\n$ln\n";
-	 my $i = $ln;
-	 $i =~ s/^>.*?\n//;
-	 $i =~ s/\n//g;
-	 $frl = length $i;
-      }
-      print OUT $ln;
-   }
-   $i++;
-}
-print "\rNumber of entries: $i     \nFirst read length: $frl\n";
-close OUT;
-
-for my $k(0..$#in_fh){print "ALERT: The file $in[$k] contains trailing entries\n" if defined readline($in_fh[$k])}
-

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

@@ -1,38 +0,0 @@
-#!/usr/bin/env perl
-#
-# @author  Luis M Rodriguez-R
-# @update  Oct-07-2015
-# @license artistic license 2.0
-#
-
-use warnings;
-use strict;
-
-$#ARGV>=0 or die "
-Usage:
-   $0 seqs.fa... > length.txt
-
-   seqs.fa	One or more FastA files.
-   length.txt	A table with the lengths of the sequences.
-
-";
-
-for my $fa (@ARGV){
-   open FA, "<", $fa or die "Cannot open file: $fa: $!\n";
-   my $def = '';
-   my $len = 0;
-   while(<FA>){
-      next if /^;/;
-      if(m/^>(\S+)\s?/){
-         print "$def\t$len\n" if $def;
-	 $def = $1;
-	 $len = 0;
-      }else{
-         s/[^A-Za-z]//g;
-	 $len+= length $_;
-      }
-   }
-   print "$def\t$len\n" if $def;
-   close FA;
-}
-

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

@@ -1,89 +0,0 @@
-#!/usr/bin/env ruby
-
-require 'optparse'
-o = {x: 'N', trim: false, wrap: 70}
-ARGV << '-h' if ARGV.empty?
-OptionParser.new do |opts|
-  opts.banner = "
-Mask sequence region(s) in a FastA file.
-
-Usage: #{$0} [options]"
-  opts.separator ''
-  opts.separator 'Mandatory'
-  opts.on('-i', '--in FILE', 'Input FastA file.'){ |v| o[:in] = v }
-  opts.on('-o', '--out FILE', 'Output FastA file.'){ |v| o[:out] = v }
-  opts.on('-r', '--regions REG1,REG2,...', Array,
-    'Regions to mask separated by commas.',
-    'Each region must be in the format "sequence_id:from..to"'
-    ){ |v| o[:reg] = v }
-  opts.separator ''
-  opts.separator 'Options'
-  opts.on('-x', '--symbol CHAR',
-    'Character used to mask the region(s)',
-    "By default: #{o[:x]}."){ |v| o[:x] = v }
-  opts.on('-t', '--trim',
-    'Trim masked regions extending to the edge of a sequence'
-    ){ |v| o[:trim] = v }
-  opts.on('-w', '--wrap INT',
-    'Line length to wrap sequences. Use 0 to generate 1-line sequences.',
-    "By default: #{o[:wrap]}."){ |v| o[:wrap] = v.to_i }
-  opts.on('-h', '--help', 'Display this screen.') do
-    puts opts
-    exit
-  end
-  opts.separator ''
-end.parse!
-abort '-i is mandatory' if o[:in].nil?
-abort '-o is mandatory' if o[:out].nil?
-abort '-r is mandatory' if o[:reg].nil?
-
-def wrap_width(txt, len)
-  return "" if txt.empty?
-  return "#{txt}\n" if len==0
-  txt.gsub(/(.{1,#{len}})/,"\\1\n")
-end
-
-# Read input sequences
-sq = {}
-File.open(o[:in], 'r') do |ifh|
-  bf = ''
-  ifh.each('>') do |i|
-    (dln, seq) = i.split(/[\n\r]+/, 2)
-    next if seq.nil?
-    id = dln.gsub(/\s.*/,  '')
-    seq.gsub!(/[\s>]/, '')
-    sq[id] = [dln, seq]
-  end
-end
-
-# Parse coordinates and mask regions
-last_id = nil
-o[:reg].each do |i|
-  m = i.match(/^(?:(.+):)?(\d+)\.\.(\d+)$/) or
-    abort "Unexpected region format: #{i}"
-  r = [m[1], m[2].to_i-1, m[3].to_i-1]
-  if r[0].nil?
-    abort "Region missing sequence ID: #{i}" if last_id.nil?
-    r[0] = last_id
-  end
-  last_id = r[0]
-  sq[r[0]] or abort "Cannot find sequence #{r[0]}"
-  r[1] <= r[2] or abort "Malformed range: #{i}"
-  if r[1] < 0 or r[2] > sq[r[0]][1].size
-    abort "Range extends beyond the edge of the sequence: #{i}"
-  end
-  sq[r[0]][1][r[1] .. r[2]] = o[:x]*(1+r[2]-r[1])
-end
-
-# Trim sequences and generate output
-ofh = File.open(o[:out], 'w')
-sq.each do |_k,v|
-  ofh.puts ">#{v[0]}"
-  if o[:trim]
-    v[1].gsub!(/^#{o[:x]}+/,'')
-    v[1].gsub!(/#{o[:x]}+$/,'')
-  end
-  ofh.print wrap_width(v[1], o[:wrap])
-end
-ofh.close
-

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

@@ -1,36 +0,0 @@
-#!/usr/bin/env perl
-#
-# @author  Luis M Rodriguez-R
-# @update  Mar-17-2016
-# @license artistic license 2.0
-#
-
-use warnings;
-use strict;
-
-$#ARGV>=1 or die "
-Usage:
-   $0 outdir seqs.fa...
-
-   outdir	Output directory for the individual files.
-   seqs.fa	One or more FastA files.
-
-";
-
-my $dir = shift @ARGV;
-
-for my $fa (@ARGV){
-   open FA, "<", $fa or die "Cannot open file: $fa: $!\n";
-   my $file = '';
-   while(<FA>){
-      next if /^;/;
-      if(m/^>(\S+)\s?/){
-	 close ONE if $file;
-         $file = $dir."/".$1.".fasta";
-	 open ONE, ">", $file or die "Cannot open file: $file: $!\n";
-      }
-      print ONE $_ if $file;
-   }
-   close ONE if $file;
-}
-

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) }