miga-base 1.2.15.1 → 1.2.15.3

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

@@ -1,152 +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}
-ARGV << '-h' if ARGV.size==0
-
-OptionParser.new do |opt|
-  opt.banner = "
-Extracts a list of sequences and/or coordinates from multi-FastA files.
-
-Usage: #{$0} [options]"
-  opt.separator ''
-  opt.separator 'Mandatory'
-  opt.on('-i', '--in PATH', 'Input FastA file.'){ |v| o[:i] = v }
-  opt.on('-o', '--out PATH', 'Output FastA file.'){ |v| o[:o] = v }
-  opt.on('-c', '--coords STRING',
-    'Comma-delimited list of coordinates (mandatory unless -C is passed).',
-    'The format of the coordinates is "SEQ:FROM..TO" or "SEQ:FROM~LEN":',
-    'SEQ: Sequence ID, or * (asterisk) to extract range from all sequences',
-    'FROM: Integer, position of the first base to include (can be negative)',
-    'TO: Integer, last base to include (can be negative)',
-    'LEN: Length of the range to extract'
-    ){ |v| o[:c] = v }
-  opt.separator ''
-  opt.separator 'Options'
-  opt.on('-C', '--coords-file PATH',
-    'File containing the coordinates, one per line.',
-    'Each line must follow the format described for -c.'){ |v| o[:C] = 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 '-o is mandatory.' if o[:o].nil?
-abort '-c is mandatory.' if o[:c].nil? and o[:C].nil?
-
-# Classses to parse coordinates
-class SeqCoords
-  attr :id, :from, :to, :length, :str
-  def initialize(str)
-    @str = str
-    m = /(\S+):(-?\d+)(~|\.\.)(-?\d+)/.match str
-    raise "Cannot parse coordinates: #{str}" if m.nil?
-    @id = m[1]
-    @from = m[2].to_i
-    if m[3] == '~'
-      @length = m[4].to_i
-    else
-      @to = m[4].to_i
-    end
-  end
-
-  def extract(id, seq)
-    return nil unless concerns? id
-    from_i = from > 0 ? from : seq.length + 1 + from
-    if to.nil?
-      seq[from_i, length]
-    else
-      to_i = to > 0 ? to : seq.length + 1 + to
-      seq[from_i .. to_i]
-    end
-  end
-
-  def concerns?(seq_id)
-    return true if id == '*'
-    return id == seq_id
-  end
-end
-
-class SeqCoordsCollection
-  class << self
-    def from_str(str)
-      c = new
-      str.split(',').each { |i| c << SeqCoords.new(i) }
-      c
-    end
-    def from_file(path)
-      c = new
-      File.open(path, 'r') do |fh|
-        fh.each{ |i| c << SeqCoords.new(i.chomp) }
-      end
-      c
-    end
-  end
-
-  attr :collection
-
-  def initialize
-    @collection = []
-  end
-
-  def <<(coords)
-    @collection << coords
-  end
-
-  def extract(id, seq)
-    @collection.map{ |c| c.extract(id, seq) }.compact
-  end
-end
-
-# 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 coordinates
-$stderr.puts 'Parsing coordinates' unless o[:q]
-@coll = o[:c].nil? ? SeqCoordsCollection.from_file(o[:C]) :
-  SeqCoordsCollection.from_str(o[:c])
-$stderr.puts "  Coordinates found: #{@coll.collection.size}"
-
-# Parse sequences
-$stderr.puts 'Parsing sequences' unless o[:q]
-@n_in = 0
-@n_out = 0
-@ofh = File.open(o[:o], 'w')
-File.open(o[:i], 'r') do |fh|
-  id = nil
-  sq = ''
-  fh.each do |ln|
-    next if ln =~ /^;/
-    if ln =~ /^>(\S+)/
-      id = $1
-      do_stuff(id, sq)
-      sq = ''
-    else
-      sq << ln
-    end
-  end
-  do_stuff(id, sq)
-end
-@ofh.close
-$stderr.puts "  Input sequences: #{@n_in}"
-$stderr.puts "  Output fragments: #{@n_out}"
-

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

@@ -1,52 +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:
-   Extracts a subset of sequences from a FastA file.
-
-.Usage: $0 [options] list.txt seqs.fa > subset.fa
-   
-   [options]
-   -r		Reverse list.  Extracts sequences NOT present in the list.
-   -q		Runs quietly.
-   -h		Prints this message and exits.
-
-   [mandatory]
-   list.txt	List of sequences to extract.
-   seqs.fa	FastA file containing the superset of sequences.
-   subset.fa	FastA file to be created.
-
-" }
-
-my %o=();
-getopts('rhq', \%o);
-my($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 { chomp; $_ => 1 } <LI>;
-close LI;
-
-print STDERR "Filtering 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+).*)/){ $good = (exists $li{$1} or exists $li{">$1"} or exists $li{$2} or exists $li{$ln}) }
-   elsif($ln =~ m/^>/){ $good=$o{r}; print STDERR "Warning: Non-cannonical defline, line $.: $ln\n" }
-   print "$ln\n" if (($good and not $o{r}) or ($o{r} and not $good));
-}
-close FA;
-

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

@@ -1,28 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-use Bio::SeqIO;
-
-my $file = $ARGV[0]; 
-my $min = $ARGV[1];
-($file and $min) or die <<HELP
-
-This script will filter a multi fastA file by length
-
-Usage "perl $0 fastafile minlenght "
-HELP
-;
-my $seq_in  = Bio::SeqIO->new( -format => 'fasta',-file => $file);
-
-while( my $seq1 = $seq_in->next_seq() ) {	
-	
-	my $id  = $seq1->primary_id;
-	chomp $id;
-	my $seq = $seq1->seq;
-	chomp $seq;
-	my $lseq = length($seq);
-	if($lseq>=$min){
-		print ">$id","\n",$seq,"\n";	
-	}
-}

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

@@ -1,60 +0,0 @@
-#!/usr/bin/env perl
-# 
-# @author  Luis M. Rodriguez-R
-# @update  Oct-07-2015
-# @license artistic license 2.0
-# 
-
-use warnings;
-use strict;
-
-my($file, $content, $stretch) = @ARGV;
-$file or die <<HELP
-
-Description:
-   Filter sequences by N-content and presence of long homopolymers.
-Usage:
-   $0 sequences.fa [content [stretch]] > filtered.fa
-Where:
-   sequences.fa	Input file in FastA format
-   content	A number between 0 and 1 indicating the maximum proportion of Ns
-   		(1 to turn off, 0.5 by default)
-   stretch	A number indicating the maximum number of consecutive identical
-   		nucleotides allowed (0 to turn off, 100 by default)
-   filtered.fa	Filtered set of sequences.
-
-HELP
-;
-($content ||= 0.5)+=0;
-($stretch ||= 100)+=0;
-
-my $good = 0;
-my $N = 0;
-
-FASTA: {
-   local $/ = "\n>";
-   open FILE, "<", $file or die "I can not open the file: $file: $!\n";
-   SEQ: while(<FILE>){
-      $N++;
-      s/^;.*//gm;
-      s/>//g;
-      my($n,$s) = split /\n/, $_, 2;
-      (my $clean = $s) =~ s/[^ACTGN]//g;
-      if($content < 1){
-         (my $Ns = $clean) =~ s/[^N]//g;
-	 next SEQ if length($Ns)>length($clean)*$content;
-      }
-      if($stretch > 0){
-         for my $nuc (qw(A C T G N)){
-	    next SEQ if $clean =~ m/[$nuc]{$stretch}/;
-	 }
-      }
-      print ">$n\n$s\n";
-      $good++;
-   }
-   close FILE;
-   print STDERR "Total sequences: $N\nAfter filtering: $good\n";
-}
-
-
-

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

@@ -1,100 +0,0 @@
-#!/usr/bin/env ruby
-
-# frozen_string_literal: true
-
-$:.push File.expand_path('../lib', __FILE__)
-require 'enveomics_rb/enveomics'
-require 'enveomics_rb/stats'
-$VERSION = 1.0
-
-o = { q: false, completeness: nil, minlen: 500, shuffle: true }
-OptionParser.new do |opts|
-  opts.version = $VERSION
-  Enveomics.opt_banner(
-    opts, 'Simulates incomplete (fragmented) drafts from complete genomes',
-    "#{File.basename($0)} -i in.fasta -o out.fasta -c 0.5 [options]"
-  )
-
-  opts.separator 'Mandatory'
-  opts.on(
-    '-i', '--in FILE',
-    'Path to the FastA file containing the complete sequences',
-    'Supports compression with .gz extension, use - for STDIN'
-  ) { |v| o[:in] = v }
-  opts.on(
-    '-o', '--out FILE', 'Path to the FastA to create',
-    'Supports compression with .gz extension, use - for STDOUT'
-  ) { |v| o[:out] = v }
-  opts.on(
-    '-c', '--completeness FLOAT',
-    'Fraction of genome completeness to simulate from 0 to 1'
-  ) { |v| o[:completeness] = v.to_f }
-
-  opts.separator ''
-  opts.separator 'Options'
-  opts.on(
-    '-m', '--minlen INT',
-    "Minimum fragment length to report. By default: #{o[:minlen]}"
-  ) { |v| o[:minlen] = v.to_i }
-  opts.on(
-    '-s', '--sorted', 'Keep fragments sorted as in the input file',
-    'By default, fragments are shuffled'
-  ) { |v| o[:shuffle] = !v }
-  opts.on('-q', '--quiet', 'Run quietly (no STDERR output)') { o[:q] = true }
-  opts.on('-h', '--help', 'Display this screen') { puts opts ; exit }
-  opts.separator ''
-end.parse!
-
-raise Enveomics::OptionError.new('-i is mandatory') if o[:in].nil?
-raise Enveomics::OptionError.new('-o is mandatory') if o[:out].nil?
-raise Enveomics::OptionError.new('-c is mandatory') if o[:completeness].nil?
-
-begin
-  # Read input sequences
-  g_id  = []
-  g_seq = []
-  ifh = reader(o[:in])
-  id = ''
-  ifh.each_line do |ln|
-    if ln =~ /^>(\S*)/
-      g_id  << $1
-      g_seq << ''
-    else
-      g_seq[g_seq.size - 1] += ln.gsub(/[^A-Za-z]/, '')
-    end
-  end
-  ifh.close
-
-  # Fragment genomes
-  f = {}
-  binlen = [1, (o[:minlen].to_f/(1.5**2)).ceil].max
-  p = [0.001, [1.0, 1.0 - (o[:completeness]/1.25 + 0.1)].min].max
-  while !g_seq.empty?
-    id  = g_id.shift
-    seq = g_seq.shift
-    gL  = seq.length
-    while !seq.empty?
-      rand_x =
-        Enveomics::Stats.r_geom(p).to_f + Enveomics::Stats.r_unif(-0.5, 0.5)
-      fL = [0, (rand_x * binlen).round].max
-      f["#{f.size+1}_#{id}"] = seq[0, fL] if fL >= o[:minlen]
-      seq = seq[(fL + 1) .. -1]
-      seq = '' if seq.nil?
-    end
-  end
-
-  # Save output
-  k = f.keys
-  k.shuffle! if o[:shuffle]
-  ofh = writer(o[:out])
-  k.each do |id|
-    ofh.puts ">#{id}"
-    ofh.puts f[id].gsub(/(\S{50})/, "\\1\n")
-  end
-  ofh.close
-rescue => err
-  $stderr.puts "Exception: #{err}\n\n"
-  err.backtrace.each { |l| $stderr.puts l + "\n" }
-  err
-end
-

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;
-}
-