miga-base 0.7.24.0 → 0.7.26.0

data/utils/enveomics/Scripts/BedGraph.tad.rb

@@ -1,93 +0,0 @@
-#!/usr/bin/env ruby
-
-require 'optparse'
-
-o = {range: 0.5, perseq: false, length: false}
-ARGV << '-h' if ARGV.empty?
-OptionParser.new do |opt|
-  opt.banner = "
-  Estimates the truncated average sequencing depth (TAD) from a BedGraph file.
-
-  IMPORTANT: This script doesn't consider zero-coverage positions if missing
-  from the file. If you produce your BedGraph file with bedtools genomecov and
-  want to consider zero-coverage position, be sure to use -bga (not -bg).
-
-  Usage: #{$0} [options]"
-  opt.separator ''
-  opt.on('-i', '--input PATH',
-    'Input BedGraph file (mandatory).'){ |v| o[:i]=v }
-  opt.on('-r', '--range FLOAT',
-    'Central range to consider, between 0 and 1.',
-    "By default: #{o[:range]} (inter-quartile range)."
-    ){ |v| o[:range]=v.to_f }
-  opt.on('-s', '--per-seq',
-    'Calculate averages per reference sequence, not total.',
-    'Assumes a sorted BedGraph file.'
-    ){ |v| o[:perseq] = v }
-  opt.on('-l', '--length',
-    'Add sequence length to the output.'){ |v| o[:length] = v }
-  opt.on('-h', '--help', 'Display this screen.') do
-    puts opt
-    exit
-  end
-  opt.separator ''
-end.parse!
-abort '-i is mandatory.' if o[:i].nil?
-
-def pad(d, idx, r)
-  idx.each do |i|
-    next if d[i].nil?
-    d[i] -= r
-    break unless d[i] < 0
-    r = -d[i]
-    d[i] = nil
-  end
-  d
-end
-
-def report(sq, d, ln, o)
-  # Estimate padding ranges
-  pad = (1.0-o[:range])/2.0
-  r = (pad*ln).round
-
-  # Pad
-  d = pad(d, d.each_index.to_a, r+0)
-  d = pad(d, d.each_index.to_a.reverse, r+0)
-
-  # Average
-  y = [0.0]
-  unless d.compact.empty?
-    s = d.each_with_index.to_a.map{ |v,i| v.nil? ? 0 : i*v }.inject(0,:+)
-    y[0] = s.to_f/d.compact.inject(:+)
-  end
-
-  # Report
-  y.unshift(sq) if o[:perseq]
-  y << ln if o[:length]
-  puts y.join("\t")
-end
-
-# Read BedGraph
-d  = []
-ln = 0
-pre_sq = nil
-File.open(o[:i], "r") do |ifh|
-  ifh.each_line do |i|
-    next if i =~ /^#/
-    r  = i.chomp.split("\t")
-    sq = r.shift
-    if o[:perseq] and !pre_sq.nil? and pre_sq!=sq
-      report(pre_sq, d, ln, o)
-      d  = []
-      ln = 0
-    end
-    r.map! { |j| j.to_i }
-    l = r[1]-r[0]
-    d[ r[2] ] ||= 0
-    d[ r[2] ]  += l
-    ln += l
-    pre_sq = sq
-  end
-end
-report(pre_sq, d, ln, o)
-

data/utils/enveomics/Scripts/BedGraph.window.rb

@@ -1,71 +0,0 @@
-#!/usr/bin/env ruby
-
-require 'optparse'
-
-o = {win: 1000}
-ARGV << '-h' if ARGV.empty?
-OptionParser.new do |opt|
-  opt.banner = "
-  Estimates the sequencing depth per windows from a BedGraph file.
-
-  IMPORTANT: This script doesn't consider zero-coverage positions if missing
-  from the file. If you produce your BedGraph file with bedtools genomecov and
-  want to consider zero-coverage position, be sure to use -bga (not -bg).
-
-  Usage: #{$0} [options]"
-  opt.separator ''
-  opt.on('-i', '--input PATH',
-    'Input BedGraph file (mandatory).'){ |v| o[:i]=v }
-  opt.on('-w', '--win INT',
-    'Window size, in base pairs.', "By default: #{o[:win]}."
-    ){ |v| o[:win]=v.to_i }
-  opt.on('-h', '--help', 'Display this screen.') do
-    puts opt
-    exit
-  end
-  opt.separator ''
-end.parse!
-abort '-i is mandatory.' if o[:i].nil?
-
-def report(d, a, b, seqs)
-  # Average
-  y = 0.0
-  unless d.compact.empty?
-    s = d.each_with_index.to_a.map{ |v,i| v.nil? ? 0 : i*v }.inject(0,:+)
-    y = s.to_f/d.compact.inject(:+)
-  end
-
-  # Report
-  puts [a, b, y, seqs.keys.join(",")].join("\t")
-end
-
-# Read BedGraph
-d  = []
-ln = 0
-a = 1
-seqs = {}
-b = o[:win]
-File.open(o[:i], "r") do |ifh|
-  ifh.each_line do |i|
-    next if i =~ /^#/
-    r  = i.chomp.split("\t")
-    sq = r.shift
-    seqs[sq] = 1
-    r.map!{ |j| j.to_i }
-    l = r[1]-r[0]
-    d[ r[2] ] ||= 0
-    d[ r[2] ]  += l
-    ln += l
-    while ln >= b
-      d[ r[2] ] -= (ln-b)
-      report(d, a, b, seqs)
-      seqs = {}
-      seqs[ sq ] = 1 if ln > b
-      d = []
-      d[ r[2] ] = (ln-b)
-      a = b + 1
-      b = a + o[:win] - 1
-    end
-  end
-end
-

data/utils/enveomics/Scripts/BlastPairwise.AAsubs.pl

@@ -1,102 +0,0 @@
-#!/usr/bin/env perl
-# 
-# @authors Konstantinos Konstantinidis (initial version)
-#          modified to work with the BLASTp 2.2.25+ m0 output by
-#          Despina Tsementzi & Luis M. Rodriguez-R
-# @updated Dec-21-2015
-#
-
-
-$/ = "Lambda     ";
-use strict;
-my %hash_depth;
-
-my @query;
-my @subject;
-my @similarity;
-my $length = "0";
-
-my($cigar_chr, $blast) = @ARGV;
-
-($cigar_chr and $blast) or die "
-.Description:
-   Counts the different AA substitutions in the best hit blast alignments, from
-   a BLASTP pairwise format output (-outfmt 0 in BLAST+, -m 0 in legacy BLAST).
-
-.Usage: $0 cigar_char blast.m0.txt > aa-subs.list
-
-   cigar_char    Use '+' for similar substitutions, use '_' for non similar
-                 substitutions
-   blast.m0.txt  Blast in 'text' format (-outfmt/-m 0).
-   aa-subs.list  A tab-delimited raw file with one substitution per row and
-                 columns:
-                 (1) Name-of-query_Name-of-subject
-		 (2) AA-in-subject
-		 (3) AA-in-query
-		 (4) Total-Align-Length
-
-";
-
-# For each blast result (i.e., for each query)
-open BLAST, "<", $blast or die "Cannot read file: $blast: $!\n";
-while(my $data=<BLAST>) {
-   $data =~ s/\r//g;
-   my ($data_q, @array_matches) = split(/>/,$data);
-   my ($name_query) = ($data_q =~ /Query\= (\S+?)(?:_GENE|\s)/);
-   my ($length_query) = ($data_q =~ /\(([\d,]+) letters/ );
-   ($length_query) = ($data_q =~ /Length=([\d,]+)/) unless $length_query;
-   $length_query =~ tr/,//d;
-   
-   # For each alignment (i.e., for each HSP),
-   # note the "last" at the end of the block,
-   # so only the best match is considered
-   foreach my $data_f (@array_matches) {
-      # Capture statistics
-      my ($length_match) = ($data_f =~ /Identities = \d+\/(\d+)/);
-      my ($identity_match) = ($data_f =~ /Identities = \d+\/\d+ \((\d+)%/);
-      my ($target_name) = ($data_f =~ /^\s?(\S+)/);
-
-      # If the alignment meets minimum requirements
-      if ($length_query >30 && ($length_match/$length_query > 0.7) && $identity_match > 60) {
-	 $data_f =~ tr/ /_/;
-	 my @array = split ("\n", $data_f);
-	 my $blanks = 0;
-	 my $prefix_size = 0;
-
-	 # For each line in the alignment
-	 for my $data_fff (@array) {	
-	    if ($data_fff =~ /(Query[:_]_+\d+_+)([^_]+)/){
-	       # Query lines
-	       $prefix_size = length($1);
-	       $length = length($2);
-	       @query = split (//, $2);
-	    }elsif ($data_fff =~ /^_{11}/){
-	       # Cigar lines
-	       @similarity = split(//, substr($data_fff, $prefix_size, $length));
-	    }elsif ($data_fff =~ /Sbjct[:_]_+\d+_+([^_]+)/){
-	       # Subject lines
-	       @subject = split(//, $1);
-	       # For each alignment column
-	       for(my $i=0; $i <= $length; $i++){
-		  if ($similarity[$i] eq $cigar_chr) {
-		     print "$name_query\_$target_name\t$subject[$i]\t$query[$i]\t$length_match\n";
-		  }
-	       }
-	       undef @query;
-	       undef @similarity;
-	       undef @subject; 
-	    }
-	    
-	    # Remove secondary alignments
-	    if ($data_fff =~ /^$/){
-	       $blanks++;
-	       last if $blanks >= 3;
-	    }else{
-	       $blanks=0;
-	    }
-	 } # for my $data_fff (@array)
-      } # if ($length_query >30 ...
-      last; # <---- So it takes only the best match!
-   } # foreach my $data_f (@array_matches)
-} # while(my $data=<>)
-

data/utils/enveomics/Scripts/BlastTab.addlen.rb

@@ -1,63 +0,0 @@
-#!/usr/bin/env ruby
-
-#
-# @author: Luis M. Rodriguez-R
-# @license: artistic license 2.0
-#
-
-require 'optparse'
-
-o = { sbj: false, q: false }
-ARGV << '-h' if ARGV.size == 0
-OptionParser.new do |opts|
-  opts.banner = "
-Appends an extra column to a BLAST with the length of the query or the subject
-sequence. You can pipe two instances to add both:
-  cat input.blast | #{$0} -f queries.fa | #{$0} -f subjects.fa -s > output.blast
-
-Usage: #{$0} [options] < input.blast > output.blast"
-  opts.separator ''
-  opts.separator 'Mandatory'
-  opts.on('-f', '--fasta FILE', 'Path to the FastA file'){ |v| o[:fasta] = v }
-  opts.separator ''
-  opts.separator 'Options'
-  opts.on('-s', '--subject',
-    'Use the subject column of the BLAST, by default the query column is used'
-    ){ o[:sbj] = true }
-  opts.on('-q', '--quiet', 'Run quietly (no STDERR output)'){ o[:q] = true }
-  opts.on('-h', '--help', 'Display this screen') do
-    puts opts
-    exit
-  end
-  opts.separator ''
-end.parse!
-abort '-f is mandatory' if o[:fasta].nil?
-
-len = {}
-id  = ''
-$stderr.puts "Reading FastA file: #{o[:fasta]}" unless o[:q]
-fh = File.open(o[:fasta], 'r')
-fh.each_line do |ln|
-   defline = /^>(\S+)/.match(ln)
-   if defline.nil?
-      ln.gsub! /[^A-Za-z]/, ''
-      abort 'Error: Unsupported format, expecting FastA' if len[id].nil?
-      len[id] = len[id] + ln.size
-   else
-      id = defline[1]
-      len[id] = 0
-   end
-end
-fh.close
-
-unless o[:q]
-  $stderr.puts 'Appending %s length column' % (o[:sbj] ? 'subject' : 'query')
-end
-ARGF.each_line do |ln|
-  ln.chomp!
-  row = ln.split /\t/
-  id = o[:sbj] ? row[1] : row[0]
-  abort "Impossible to find sequence of #{id}" if len[id].nil?
-  puts "#{ln}\t#{len[id]}"
-end
-

data/utils/enveomics/Scripts/BlastTab.advance.bash

@@ -1,48 +0,0 @@
-#!/bin/bash
-
-#
-# @author  Luis M. Rodriguez-R
-# @update  Mar-23-2016
-# @license artistic license 2.0
-#
-
-if [[ ! $2 ]] ; then
-   echo "
-.DESCRIPTION
-   Calculates the percentage of a partial BLAST result. The
-   value produced slightly subestimates the actual advance,
-   due to un-flushed output and trailing queries that could
-   be processed but generate no results.
-
-.USAGE
-   $0 blast.txt qry.fasta
-
-   blast.txt	Incomplete Tabular BLAST output.
-   qry.fasta	FastA file with query sequences.
-";
-   exit 1;
-fi
-
-if [[ ! -r $1 ]]; then
-   echo "Cannot open file: $1";
-   exit 1;
-fi
-
-if [[ ! -r $2 ]]; then
-   echo "Cannot open file: $2";
-   exit 1;
-fi
-
-LAST_Q=`tail -n 2 $1 | head -n 1 | awk '{print $1}'`
-LAST_Q_NO=`grep -n "^>$LAST_Q\\( \\|$\\)" $2 | sed -e 's/:.*//'`
-if [[ ! $LAST_Q_NO ]]; then
-   echo "Cannot find sequence: $LAST_Q";
-   echo "Make sure you are providing the right query file.";
-   exit 1;
-fi
-TOTAL_Q_NO=`cat $2 | wc -l | sed -e 's/ *//'`
-let PERC=100*$LAST_Q_NO/$TOTAL_Q_NO
-
-echo "$PERC%: $LAST_Q_NO / $TOTAL_Q_NO"
-exit 0;
-

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

@@ -1,55 +0,0 @@
-#!/usr/bin/env perl
-
-#
-# @author: Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>
-# @license: artistic license 2.0
-# @last_update: Mar-23-2015
-#
-
-use strict;
-use warnings;
-
-die "
-Usage:
-   sort blast.txt ... | $0 > blast.bh.txt
-   $0 blast_sorted.txt ... > blast.bh.txt
-   $0 -h|--help|-?
-
-   blast.txt ...	One or more files in Tabular BLAST format.
-   blast_sorted.txt ...	One or more files in Tabular BLAST format pre-sorted.
-   blast.bh.txt		Output file in BLAST format containing best-hits only.
-   -h|--help|-?		Any of these flags trigger this help message and exits.
-
-   NOTE: This script assumes that the BLAST is sorted.  Because it can read
-   from the STDIN, calling this script without arguments cause it to still until
-   killed or until an EOF (^D) is presented.
-
-" if exists $ARGV[0] and $ARGV[0] =~ /^\-?\-(h(elp)?|\?)/i;
-
-my $last_qry = '';
-my @best_res;
-
-sub best_result($$){
-   my($r1, $r2)=@_;
-   return $r1 unless $r2;
-   return $r1->[11] > $r2->[11] ? @$r1 : @$r2;
-}
-
-my $i=0;
-while(<>){
-   chomp;
-   #print STDERR " Reading entry $i...                             \r" unless $i%1000;
-   my @res = split /\t/;
-   die "\nCannot parse BLAST line $.: $_\n" unless exists $res[1];
-   if($last_qry eq $res[0]){
-      @best_res = &best_result(\@res, \@best_res);
-   }else{
-      print join("\t", @best_res), "\n" if $#best_res>0;
-      @best_res = @res;
-      $last_qry = $res[0];
-   }
-}
-print join("\t", @best_res), "\n" if @best_res;
-
-
-

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

@@ -1,104 +0,0 @@
-#!/usr/bin/env perl
-
-# @author: Luis M. Rodriguez-R
-# @license: Artistic-2.0
-
-use warnings;
-use strict;
-use List::Util qw/min max/;
-use Getopt::Std;
-
-sub HELP_MESSAGE { die "
-
-Description:
-  Generates a list of hits from a BLAST result concatenating the subject
-  sequences.  This can be used, e.g., to analyze BLAST results against
-  draft genomes.
-
-Usage:
-  $0 [options] seq.fa map.bls
-
-  seq.fa	Subject sequences (ref) in FastA format.
-  map.bls	Mapping of the reads to the reference in BLAST Tabular
-   		format.
-   
-  Options:
-  -i <float>	Minimum identity to report a result.  By default: 70.
-  -l <int>	Minimum alignment length to report a result.  By default: 60.
-  -s		The FastA provided is to be treated as a subset of the subject.
-   		By default, it expects all the BLAST subjects to be present in
-		the FastA.
-  -q		Run quietly.
-  -h		Display this message and exit.
-   
-  This script creates two files using <map.bls> as prefix with extensions
-  .rec (for the recruitment plot) and .lim (for the limits of the different
-  sequences in <seq.fa>).
-
-";}
-
-my %o;
-getopts('i:l:sqh', \%o);
-my($fa, $map) = @ARGV;
-($fa and $map) or &HELP_MESSAGE;
-$o{h} and &HELP_MESSAGE;
-$o{i} ||= 70;
-$o{l} ||= 60;
-
-my %seq = ();
-my @seq = ();
-my $tot = 0;
-
-SEQ: {
-  print STDERR "== Reading reference sequences\n" unless $o{q};
-  open FA, "<", $fa or die "Cannot read the file: $fa: $!\n";
-  my $cur_seq = '';
-  while(<FA>){
-    chomp;
-    if(m/^>(\S+)/){
-      my $c = $1;
-      $seq{$c} = exists $seq{$cur_seq} ? $seq{$cur_seq}+1 : 1;
-      push @seq, $c;
-      $cur_seq = $c;
-    }else{
-      s/[^A-Za-z]//g;
-      $seq{$cur_seq} += length $_;
-    }
-  }
-  close FA;
-  print STDERR " Found ".(scalar @seq)." sequences.\n" unless $o{q};
-}
-
-open LIM, ">", "$map.lim" or die "Cannot create the file: $map.lim: $!\n";
-my $l = 0;
-for my $s (@seq){
-  print LIM "$s\t".(++$l)."\t$seq{$s}\n";
-  ($l, $seq{$s}) = ($seq{$s}, $l);
-}
-close LIM;
-
-MAP: {
-  print STDERR "== Reading mapping\n" unless $o{q};
-  open BLS, "<", $map or die "Cannot read the file: $map: $!\n";
-  open REC, ">", "$map.rec" or die "Cannot create the file: $map.rec: $!\n";
-  RESULT: while(<BLS>){
-    chomp;
-    my @ln = split /\t/;
-    $ln[11] or die "Cannot parse line $map:$.: $_\n";
-    next unless $ln[3]>=$o{l};
-    next unless $ln[2]>=$o{i};
-    unless(exists $seq{$ln[1]}){
-      die "Cannot find the subject sequence: $ln[1]\n" unless $o{s};
-      next RESULT;
-    }
-    my $start = $seq{$ln[1]}+min($ln[8], $ln[9]);
-    my $end   = $seq{$ln[1]}+max($ln[8], $ln[9]);
-    print REC "$start\t$end\t$ln[2]\t$ln[11]\t$ln[0]",
-          (exists($ln[13])?"\t".($ln[2]*$ln[3]/min($ln[12],$ln[13]))."\t":
-          exists($ln[12])?"\t".($ln[2]*$ln[3]/$ln[12])."\t":""),"\n";
-  }
-  close BLS;
-  close REC;
-  print STDERR " done.\n" unless $o{q};
-}
-