miga-base 0.7.23.0 → 0.7.25.3

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

@@ -1,76 +0,0 @@
-#!/usr/bin/env ruby
-
-#
-# @author  Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>
-# @update  Mar-23-2016
-# @license artistic license 2.0
-#
-
-require "optparse"
-
-o = {:cog=>false, :desc=>false, :q=>false, :w=>true}
-ARGV << "-h" if ARGV.size==0
-OptionParser.new do |opts|
-   opts.banner = "Replaces the COG gene IDs in a BLAST for the COG category."
-   opts.separator ""
-   opts.separator "Mandatory"
-   opts.on("-w", "--whog FILE", "Path to the whog file."){ |v| o[:whog]=v }
-   opts.on("-i", "--blast FILE",
-      "Path to the Tabular BLAST file with COG IDs as subject."
-      ){ |v| o[:blast]=v }
-   opts.separator ""
-   opts.separator "Optional"
-   opts.on("-g", "--cog",
-      "If set, returns the COG ID, not the COG category."){ o[:cog]=true }
-   opts.on("-d", "--desc",
-      "Includes COG description (requires -g/--cog)."){ o[:desc]=true }
-   opts.on("-n", "--noverbose", "Run quietly, but show warnings."){ o[:q]=true }
-   opts.on("-q", "--quiet", "Run quietly."){ o[:q]=true; o[:w]=false }
-   opts.on("-h", "--help", "Display this screen") do
-      puts opts
-      exit
-   end
-   opts.separator ""
-end.parse!
-
-abort "-w/--whog is mandatory." if o[:whog].nil?
-abort "-i/--blast is mandatory." if o[:blast].nil?
-
-$stderr.puts "Parsing whog file." unless o[:q]
-cat = {}
-curCats = []
-fh = File.open o[:whog], "r"
-while ln=fh.gets
-   ln.chomp!
-   next if /^\s*$/.match ln
-   if m=/^\[([A-Z]+)\] (COG\d+) (.*)/.match(ln)
-      curCats = o[:cog] ? [ m[2]+(o[:desc]?" #{m[3]}":"") ] : m[1].split(//)
-   elsif /^_+$/.match ln
-      curCats = []
-   elsif m=/^\s+(?:.+?:\s+)?(.*)/.match(ln)
-      m[1].split(/\s+/).each do |g|
-         cat[g] ||= []
-	 curCats.each { |i| cat[g] << i }
-      end
-   else
-      abort "Impossible to parse line #{$.}: #{ln}"
-   end
-end
-fh.close
-
-$stderr.puts "Parsing BLAST." unless o[:q]
-fh = File.open(o[:blast], "r")
-while ln=fh.gets
-   row = ln.split(/\t/)
-   if cat[ row[1] ].nil?
-      $stderr.puts "Warning: line #{$.}: #{row[1]}: " +
-	 "Impossible to find category.\n" if o[:w]
-   else
-      cat[ row[1] ].each do |c|
-         row[1] = c
-	 puts row.join("\t")
-      end
-   end
-end
-fh.close
-

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

@@ -1,47 +0,0 @@
-#!/usr/bin/env perl
-#
-# @author: Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>
-# @update: Mar-23-2015
-# @license: artistic license 2.0
-#
-
-use warnings;
-use strict;
-use Getopt::Std;
-
-my %o;
-getopts('si', \%o);
-my($list, $blast) = @ARGV;
-
-($list and $blast) or die "
-.Description:
-   Extracts a subset of hits (queries or subjects) from a tabular BLAST.
-
-.Usage: $0 [options] list.txt blast.txt > subset.txt
-   
-   Options:
-      -s	If set, assumes that list.txt contains subject IDs.
-   		By default: assumes query IDs.
-      -i	If set, reports the inverse of the list (i.e., reports
-      		only hits absent in the list).
-
-   list.txt	List of IDs to extract.
-   blast.txt	Tabular BLAST file containing the superset of hits.
-   subset.txt	Tabulat BLAST file to be created.
-
-";
-
-open LI, "<", $list or die "Cannot read file: $list: $!\n";
-my %li = map { chomp; $_ => 1 } <LI>;
-close LI;
-
-open BLAST, "<", $blast or die "Cannot read file: $blast: $!\n";
-while(my $ln = <BLAST>){
-   chomp $ln;
-   my @ln = split("\t", $ln);
-   my $good = exists $li{$ln[ ($o{s} ? 1 : 0) ]};
-   $good = not $good if $o{i};
-   print "$ln\n" if $good;
-}
-close BLAST;
-

data/utils/enveomics/Scripts/BlastTab.kegg_pep2path_rest.pl

@@ -1,194 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-use LWP::Simple;
-use JSON;
-use File::Copy;
-
-my($blast, $cache_file, $max_cache) = @ARGV;
-($blast) or die "
-Description:
-   Takes a BLAST against KEGG_PEP (or KO) and retrieves the pathways in which the subject
-   peptides are involved.
-
-Usage:
-   $0 blast.txt[ cache_file] > output.txt
-
-   blast.txt	Input (filtered) BLAST file.
-   cache_file	(optional) File containing the saved cache.  If unset, the
-   		cache won't be recoverable across instances of this script.
-		It is strongly recommended to set a file.  Multiple
-		parallel instances of this script may use the same cache
-		file.
-   output.txt	Tab-delimited output file, with the columns:
-   		 o Query ID
-		 o Subject ID
-		 o Pathway ID
-		 o Pathway (reference) description
-		 o Organism
-
-";
-
-$max_cache ||= 0;
-$cache_file ||= "";
-
-sub read_cache($){
-   my ($cache_file) = @_;
-   my $cache = {};
-   my $n = 0;
-   if($cache_file and -s $cache_file){
-      local $/;
-      my $json = "";
-      while(-e "$cache_file.tmp"){
-         print STDERR "Locked cache (read), waiting 1 sec.\n";
-	 sleep 1;
-      }
-      open CACHE, "<", $cache_file or die "Cannot read file: $cache_file: $!\n";
-      while(<CACHE>){ $json.=$_ }
-      close CACHE;
-      $cache = decode_json($json);
-      $n = scalar keys %$cache;
-   }
-   return ($cache, $n);
-}
-
-sub write_cache($$){
-   my($cache, $cache_file) = @_;
-   if($cache_file){
-      # Get previously saved entries.
-      my($cache2, $cache_n2) = &read_cache($cache_file);
-      for my $k (keys %$cache2){
-	 $cache->{$k} ||= $cache2->{$k} unless $k eq "###:paths";
-      }
-      $cache->{'###:paths'} ||= {};
-      for my $p (keys %{$cache2->{'###:paths'}}){
-         $cache->{'###:paths'}->{$p} ||= $cache2->{'###:paths'}->{$p};
-      }
-      # Save merged cache.
-      if(-s $cache_file){ copy $cache_file, "$cache_file.pre" or die "Cannot create file: $cache_file.tmp: $!\n" }
-      my $json = encode_json($cache);
-      while(-e "$cache_file.tmp"){
-         print STDERR "Locked cache (write), waiting 1 sec.\n";
-	 sleep 1;
-      }
-      open CACHE, ">", "$cache_file.tmp" or die "Cannot create file: $cache_file.tmp: $!\n";
-      print CACHE $json;
-      close CACHE;
-      copy "$cache_file.tmp", $cache_file or die "Cannot create file: $cache_file: $!\n";
-      unlink "$cache_file.tmp" or die "Cannot unlink file: $cache_file.tmp: $!\n";
-   }
-}
-
-sub download_pathways($$){
-   my($cache, $ids) = @_;
-   my @todownload = ();
-   for my $id (@$ids){
-      push @todownload, $id unless exists $cache->{'###:paths'}->{$id};
-   }
-   while($#todownload>=0){
-      my @downloading = splice(@todownload, 0, 100);
-      my $path = get "http://rest.kegg.jp/list/".join("+", @downloading);
-      if($path){
-	 chomp $path;
-	 for my $p (split /\n/, $path){
-	    my @wl = split /\t/, $p;
-	    $wl[1] =~ s/ - /\t/;
-	    $cache->{'###:paths'}->{$wl[0]} = $wl[1];
-	 }
-      }
-   }
-   return $cache;
-}
-
-sub download($$){
-   my($cache, $todownload) = @_;
-   $cache->{'###:paths'} ||= {};
-   return $cache unless $#$todownload>=0;
-   $cache->{$_} = [] for @$todownload;
-   my $list = get "http://rest.kegg.jp/link/pathway/".join("+", @$todownload);
-   $list ||= "";
-   chomp $list;
-   my @pathids = ();
-   for my $res (split /\n/, $list){
-      my @rel = split /\t/, $res;
-      $#rel==1 or die "Unexpected number of columns:\n$res\n";
-      my $id = $rel[1];
-      push @pathids, $id;
-      unless(exists $cache->{$rel[0]}){
-	 #print STDERR "Request/response difference in ID: ".$rel[0].", searching match.\n";
-         for my $id (@$todownload){
-	    $rel[0] = $id if lc $id eq lc $rel[0];
-	 }
-	 die "Cannot find corresponding request.\n" unless exists $cache->{$rel[0]};
-      }
-      push @{ $cache->{$rel[0]} }, $id;
-   }
-   return &download_pathways($cache, \@pathids);
-}
-
-sub print_out($$){
-   my($cache, $hits) = @_;
-   for my $hit (@$hits){
-      die "Impossible to find gene in cache: ".$hit->[1]."\n" unless exists $cache->{$hit->[1]};
-      for my $path (@{$cache->{$hit->[1]}}){
-	 next if $path =~ /^path:ko\d/;
-	 unless(exists $cache->{'###:paths'}->{$path}){
-	    print STDERR "Cannot find pathway in cache: $path (from ".$hit->[1]."), emergency download\n";
-	    $cache = &download_pathways($cache, [$path]);
-	    die "Impossible to find pathway: $path.\n" unless exists $cache->{'###:paths'}->{$path};
-	 }
-	 print "", join("\t", $hit->[0], $hit->[1], $path, $cache->{'###:paths'}->{$path}), "\n";
-      }
-   }
-}
-
-print STDERR "Loading cache.\n";
-my ($cache, $n) = &read_cache($cache_file);
-print STDERR "   $n entries loaded.\n";
-my @nopath = ();
-for my $k (keys %$cache){
-   next if $k eq "###:paths";
-   for my $p (@{ $cache->{$k} }){
-      push @nopath, $p unless exists $cache->{'###:paths'}->{$p};
-   }
-}
-if($#nopath>=0){
-   print STDERR "   Sanitizing ".@nopath." pathways in cache.\n";
-   while($#nopath>=0){
-      my @paths = ();
-      for(1 .. 15){ push @paths, shift @nopath unless $#nopath==-1 }
-      $cache = &download_pathways($cache, \@paths);
-   }
-   &write_cache($cache, $cache_file);
-}
-
-my $lines=0;
-my $downs=0;
-my @buff = ();
-my @todownload = ();
-print STDERR "Mapping genes.\n";
-open BLAST, "<", $blast or die "Cannot read file: $blast: $!\n";
-while(<BLAST>){
-   chomp;
-   my @l = split /\t/;
-   print STDERR "   Mapping line ".(++$lines).". \r";
-   unless(($#todownload+2)%100){
-      print STDERR "+\r";
-      print STDERR " *\r" unless ++$downs%10;
-      $cache = &download($cache, \@todownload);
-      @todownload = ();
-      &print_out($cache, \@buff);
-      @buff = ();
-      &write_cache($cache, $cache_file) unless $downs%10;
-   }
-   push @buff, \@l;
-   push @todownload, $l[1] unless exists $cache->{$l[1]};
-}
-print STDERR "\nDone.\n";
-close BLAST;
-
-$cache = &download($cache, \@todownload);
-&print_out($cache, \@buff);
-&write_cache($cache, $cache_file);
-

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

@@ -1,104 +0,0 @@
-#!/usr/bin/env perl
-
-#
-# @author Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>
-# @update Mar-23-2015
-# @license artistic license 2.0
-#
-
-use warnings;
-use strict;
-use Getopt::Std;
-
-
-sub HELP_MESSAGE { die "
-Usage:
-   $0 [options] genes.txt blast.txt ... > blast_metaxa.txt
-
-   genes.gff2		File containing the genes in any supported format
-   			(see option -f).
-   blast.txt ...	One or more tabular BLAST files.
-   blast_metaxa.txt	Input file for MeTaxa.
-
-   Options:
-   -l <float>		Minimum fraction of the gene aligned to consider a
-   			hit.  By default: 0.75.  Ignored if -f 'no'.
-   -f <str>		Format of the genes prediction.  Any of:
-   			 o gff2: GFF v2 as produced by MetaGeneMark.hmm.
-			 o gff3: GFF v3 with id field in the last column.
-			 o tab: Tabular file with columns gene, gene length,
-			   and contig.
-			 o no: Ignores genes file.
-			By default: gff2.
-   -q			Run quietly.
-   -h			Display this message and exit.
-
-";}
-
-my %o;
-getopts('l:f:qh',\%o);
-my($gff, @blasts) = @ARGV;
-($gff and $#blasts>=0) or &HELP_MESSAGE;
-$o{h} and &HELP_MESSAGE;
-$o{f} ||= "gff2";
-$o{f} = lc $o{f};
-$o{l} ||= 0.75;
-
-my %gene;
-if($o{f} ne 'no'){
-   print STDERR "Reading genes collection.\n" unless $o{q};
-   open GFF, "<", $gff or die "Cannot read file: $gff: $!\n";
-   while(<GFF>){
-      next if /^#/;
-      next if /^\s*$/;
-      chomp;
-      my @ln = split /\t/;
-      if($o{f} eq 'gff2'){
-	 exists $ln[8] or die "Cannot parse line $.: $_\n";
-	 my $id = $ln[8];
-	 $id =~ s/gene_id /gene_id_/;
-	 $ln[0] =~ s/ .*//;
-	 $gene{$id} = [$ln[0], (1+$ln[4]-$ln[3])/3];
-      }elsif($o{f} eq 'gff3'){
-	 exists $ln[8] or die "Cannot parse line $.: $_\n";
-	 $ln[8] =~ /id=([^;]+)/ or die "Cannot parse line $.: $_\n";
-	 my $id = $1;
-	 $ln[0] =~ s/ .*//;
-	 $gene{$id} = [$ln[0], (1+$ln[4]-$ln[3])/3];
-      }elsif($o{f} eq 'tab'){
-         exists $ln[2] or die "Cannot parse line $.: $_\n";
-	 $ln[1]+0 or die "$ln[0]: Length zero.\n";
-         $gene{$ln[0]} = [$ln[2], $ln[1]/3];
-      }else{
-         die "Unsupported format: ".$o{f}.".\n";
-      }
-   }
-   close GFF;
-}
-
-my $i=0;
-my $p=0;
-print STDERR "Generating MeTaxa input.\n" unless $o{q};
-for my $blast (@blasts){
-   print STDERR "  o $blast\n" unless $o{q};
-   open BLAST, "<", $blast or die "Cannot read file: $blast: $!\n";
-   while(<BLAST>){
-      chomp;
-      my @l = split /\t/;
-      $i++;
-      my $ctg;
-      if($o{f} eq 'no'){
-         $ctg = $l[0];
-      }else{
-	 exists $gene{$l[0]} or die "Cannot find contig for gene $l[0].\n";
-	 next unless $l[3] >= $o{l}*$gene{$l[0]}->[1];
-	 $ctg = $gene{$l[0]}->[0];
-      }
-      $l[1] =~ m/gi\|(\d+)\|/ or die "Cannot parse GI in $l[1].\n";
-      print "".join("\t", @l, $ctg, $l[0], $1)."\n";
-      $p++;
-   }
-   close BLAST;
-}
-print STDERR " Found $i results, reported $p.\n" unless $o{q};
-

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

@@ -1,157 +0,0 @@
-#!/usr/bin/env ruby
-
-#
-# @author Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>
-# @update: Jul-29-2015
-# @license artistic license 2.0
-#
-
-require 'optparse'
-
-opts = {:minscore=>0, :besthits=>0, :orient=>0, :sisprefix=>"_"}
-ARGV << '-h' if ARGV.size==0
-OptionParser.new do |opt|
-   opt.separator "Identifies the best hits of paired-reads."
-   opt.separator ""
-   opt.on("-i", "--blast FILE", "Input BLAST file."){ |v| opts[:blast]=v }
-   opt.on("-s", "--minscore FLOAT", "Minimum (summed) Bit-Score to consider a pair-match."){ |v| opts[:minscore] = v.to_f }
-   opt.on("-b", "--besthits INT", "Outputs top best-hits only (use 0 to output all the paired hits)."){ |v| opts[:besthits]=v.to_i }
-   opt.on("-o", "--orient INT", "Checks the orientation of the hit.  Values are: 0, no checking; 1, same direction; 2,",
-   		"inwards; 3, outwards; 4, different direction (i.e., 2 or 3)."){ |v| opts[:orient]=v.to_i }
-   opt.on("-p", "--sisprefix STR", "Sister read number prefix in the name of the reads.  Escape characters as dots (\\.),",
-   		"parenthesis (\\(, \\), \\[, \\]), or other characters with special meaning in regular expressions",
-		"(\\*, \\+, \\^, \\$, \\|).  This prefix allows regular expressions (for example, use ':|\\.' to use any of",
-		"colon or dot).  Notice that the prefix will not be included in the base name reported in the output."){ |v| opts[:sisprefix]=v }
-   opt.on("-h","--help","Display this screen") do
-      puts opt
-      exit
-   end
-   opt.separator ""
-   opt.separator "Output:"
-   opt.separator "   Tab-delimited flat file, with the following columns:"
-   opt.separator "   1. Query ID (without the \"sister\" identifier)."
-   opt.separator "   2. Subject ID."
-   opt.separator "   3. Bit score (summed from both sister reads)."
-   opt.separator "   4/5. From/To (subject) coordinates for read 1."
-   opt.separator "   6/7. From/To (subject) coordinates for read 2."
-   opt.separator "   8. Reads orientation (1: same direction, 2: inwards, 3: outwards)."
-   opt.separator "   9. Estimated insert size."
-   opt.separator ""
-   opt.separator "Important note: This script assumes that paired hits are next to each other."
-   opt.separator "   If this is not the case (e.g., because the blast was concatenated),"
-   opt.separator "   you must sort the input before running this script."
-   opt.separator ""
-end.parse!
-abort "-i/--blast is mandatory." if opts[:blast].nil?
-abort "-i/--blast must exist." unless File.exists? opts[:blast]
-
-class SingleHit
-   attr_reader :sbj, :score, :orient, :sfrom, :sto, :qfrom, :qto
-   def initialize(blast_ln)
-      blast_ln.chomp!
-      ln = blast_ln.split("\t")
-      @sbj    = ln[1]
-      @score  = ln[11].to_f
-      @qfrom  = ln[6].to_i
-      @qto    = ln[7].to_i
-      @sfrom  = ln[8].to_i
-      @sto    = ln[9].to_i
-      @orient = @sfrom < @sto ? 1 : -1;
-   end
-end
-class DoubleHit
-   attr_reader :name, :sbj, :score, :orient, :hitA, :hitB
-   def initialize(name, hitA, hitB)
-      raise "Trying to set DoubleHit from hits with different subjects" unless hitA.sbj == hitB.sbj
-      @name = name
-      @hitA = hitA
-      @hitB = hitB
-      @sbj = hitA.sbj
-      @score = hitA.score + hitB.score
-      @orient = (hitA.orient == hitB.orient ? 1:
-      		((hitA.orient>0 and hitB.orient<0) ? 2: 3))
-   end
-   def to_s
-      coords = [@hitA.sfrom, @hitB.sfrom, @hitA.sto, @hitB.sto]
-      @name + "\t" + @sbj + "\t" + @score.to_s + "\t" +
-      	@hitA.sfrom.to_s + "\t" + @hitA.sto.to_s + "\t" +
-      	@hitB.sfrom.to_s + "\t" + @hitB.sto.to_s + "\t" +
-	@orient.to_s + "\t" + (coords.max-coords.min).to_s + "\n"
-   end
-end
-class PairedHits
-   attr_reader :name, :hitsA, :hitsB
-   @@minscore = 0
-   @@orient = 0
-   @@besthits = 0
-   def initialize(name)
-      @name = name
-      @hitsA = []
-      @hitsB = []
-      @hits  = []
-   end
-   def hits
-      @hits = []
-      # Search for paired hits
-      @hitsA.each do |hitA|
-         @hitsB.each do |hitB|
-	    if hitA.sbj == hitB.sbj
-	       hit = DoubleHit.new(@name, hitA, hitB)
-	       next if hit.score <= @@minscore # Minimum bit-score check
-	       next if ((1 .. 3).include?(@@orient) and @@orient != hit.orient) # "typical" orientation check
-	       next if (@@orient == 4 and not((2 .. 3).include?(hit.orient))) # "different-orientation" check
-	       @hits.push(hit)
-	    end
-	 end
-      end
-      # Sort the hits
-      @hits.sort! {|x,y| x.score <=> y.score }
-      if @@besthits==0
-         @hits
-      else
-         @hits.take(@@besthits)
-      end
-   end
-   def hitsX(x)
-      if x == 1
-         @hitsA
-      else
-         @hitsB
-      end
-   end
-   # Class methods
-   def PairedHits.minscore=(value)
-      @@minscore = value
-   end
-   def PairedHits.orient=(value)
-      @@orient = value
-   end
-   def PairedHits.besthits=(value)
-      @@besthits = value
-   end
-end
-
-PairedHits.minscore = opts[:minscore]
-PairedHits.orient   = opts[:orient]
-PairedHits.besthits = opts[:besthits]
-
-begin
-   f = File.open(opts[:blast], "r")
-   currPair = PairedHits.new("  ")
-   while(ln = f.gets)
-      m = /^([^\s]*)(?:#{opts[:sisprefix]})([12])/.match(ln)
-      raise "Impossible to parse read name in line #{$.} using sister prefix '#{opts[:sisprefix]}':\n#{ln}"  unless m
-      if m[1] != currPair.name
-	 currPair.hits.each { |hit| puts hit.to_s }
-	 currPair = PairedHits.new(m[1])
-      end
-      currPair.hitsX(m[2].to_i).push(SingleHit.new(ln));
-   end
-   currPair.hits.each { |hit| puts hit.to_s }
-   f.close
-rescue => err
-   $stderr.puts "Exception: #{err}\n\n"
-   err.backtrace.each { |l| $stderr.puts l + "\n" }
-   err
-end
-