miga-base 0.3.0.6 → 0.3.0.7

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
checksums.yaml CHANGED
@@ -1,7 +1,7 @@
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data/lib/miga/project.rb CHANGED
@@ -273,9 +273,10 @@ class MiGA::Project < MiGA::MiGA
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  def add_result(name, save=true)
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  return nil if @@RESULT_DIRS[name].nil?
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  base = "#{path}/data/#{@@RESULT_DIRS[name]}/miga-project"
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- return MiGA::Result.load("#{base}.json") unless save
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- return nil unless result_files_exist?(base, ".done")
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- r = send("add_result_#{name}", base)
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+ r_pre = MiGA::Result.load("#{base}.json")
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+ return r_pre if (r_pre.nil? and not save) or not r_pre.nil?
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+ r = result_files_exist?(base, ".done") ?
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+ send("add_result_#{name}", base) : nil
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  r.save unless r.nil?
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  r
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  end
data/lib/miga/version.rb CHANGED
@@ -10,7 +10,7 @@ module MiGA
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  # - Float representing the major.minor version.
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  # - Integer representing gem releases of the current version.
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  # - Integer representing minor changes that require new version number.
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- VERSION = [0.3, 0, 6]
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+ VERSION = [0.3, 0, 7]
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  ##
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  # Nickname for the current major.minor version.
@@ -18,7 +18,7 @@ module MiGA
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  ##
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  # Date of the current gem release.
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- VERSION_DATE = Date.new(2017, 8, 24)
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+ VERSION_DATE = Date.new(2017, 8, 25)
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  ##
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  # Reference of MiGA.
@@ -0,0 +1,56 @@
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+ #!/usr/bin/env perl
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+ #
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+ # @author: Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>
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+ # @update: Oct 07 2015
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+ # @license: artistic license 2.0
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+ #
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+ use strict;
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+ use warnings;
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+ use List::Util qw/sum min max/;
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+
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+ my ($seqs, $minlen, $n__) = @ARGV;
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+ $seqs or die "
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+ Description:
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+ Calculates the N50 value of a set of sequences. Alternatively, it
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+ can calculate other N** values. It also calculates the total number
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+ of sequences and the total added length.
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+
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+ Usage:
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+ $0 seqs.fa[ minlen[ **]]
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+
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+ seqs.fa A FastA file containing the sequences.
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+ minlen (optional) The minimum length to take into consideration.
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+ By default: 0.
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+ ** Value N** to calculate. By default: 50 (N50).
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+ ";
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+ $minlen ||= 0;
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+ $n__ ||= 50;
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+
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+ my @len = ();
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+ open SEQ, "<", $seqs or die "Cannot open file: $seqs: $!\n";
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+ while(<SEQ>){
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+ if(/^>/){
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+ push @len, 0;
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+ }else{
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+ next if /^;/;
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+ chomp;
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+ s/\W//g;
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+ $len[-1]+=length $_;
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+ }
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+ }
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+ close SEQ;
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+ @len = sort { $a <=> $b } map { $_>=$minlen?$_:() } @len;
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+ my $tot = (sum(@len) || 0);
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+
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+ my $thr = $n__*$tot/100;
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+ my $pos = 0;
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+ for(@len){
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+ $pos+= $_;
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+ if($pos>=$thr){
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+ print "N$n__: $_\n";
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+ last;
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+ }
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+ }
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+ print "Sequences: ".scalar(@len)."\n";
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+ print "Total length: $tot\n";
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+
@@ -0,0 +1,60 @@
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+ #!/usr/bin/env perl
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+ #
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+ # @author Luis M. Rodriguez-R
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+ # @update Oct-07-2015
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+ # @license artistic license 2.0
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+ #
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+
8
+ use warnings;
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+ use strict;
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+
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+ my($file, $content, $stretch) = @ARGV;
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+ $file or die <<HELP
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+
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+ Description:
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+ Filter sequences by N-content and presence of long homopolymers.
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+ Usage:
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+ $0 sequences.fa [content [stretch]] > filtered.fa
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+ Where:
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+ sequences.fa Input file in FastA format
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+ content A number between 0 and 1 indicating the maximum proportion of Ns
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+ (1 to turn off, 0.5 by default)
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+ stretch A number indicating the maximum number of consecutive identical
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+ nucleotides allowed (0 to turn off, 100 by default)
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+ filtered.fa Filtered set of sequences.
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+
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+ HELP
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+ ;
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+ ($content ||= 0.5)+=0;
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+ ($stretch ||= 100)+=0;
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+
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+ my $good = 0;
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+ my $N = 0;
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+
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+ FASTA: {
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+ local $/ = "\n>";
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+ open FILE, "<", $file or die "I can not open the file: $file: $!\n";
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+ SEQ: while(<FILE>){
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+ $N++;
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+ s/^;.*//gm;
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+ s/>//g;
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+ my($n,$s) = split /\n/, $_, 2;
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+ (my $clean = $s) =~ s/[^ACTGN]//g;
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+ if($content < 1){
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+ (my $Ns = $clean) =~ s/[^N]//g;
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+ next SEQ if length($Ns)>length($clean)*$content;
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+ }
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+ if($stretch > 0){
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+ for my $nuc (qw(A C T G N)){
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+ next SEQ if $clean =~ m/[$nuc]{$stretch}/;
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+ }
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+ }
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+ print ">$n\n$s\n";
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+ $good++;
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+ }
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+ close FILE;
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+ print STDERR "Total sequences: $N\nAfter filtering: $good\n";
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+ }
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+
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+
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+
@@ -0,0 +1,38 @@
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+ #!/usr/bin/env perl
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+ #
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+ # @author Luis M Rodriguez-R
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+ # @update Oct-07-2015
5
+ # @license artistic license 2.0
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+ #
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+
8
+ use warnings;
9
+ use strict;
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+
11
+ $#ARGV>=0 or die "
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+ Usage:
13
+ $0 seqs.fa... > length.txt
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+
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+ seqs.fa One or more FastA files.
16
+ length.txt A table with the lengths of the sequences.
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+
18
+ ";
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+
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+ for my $fa (@ARGV){
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+ open FA, "<", $fa or die "Cannot open file: $fa: $!\n";
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+ my $def = '';
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+ my $len = 0;
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+ while(<FA>){
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+ next if /^;/;
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+ if(m/^>(\S+)\s?/){
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+ print "$def\t$len\n" if $def;
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+ $def = $1;
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+ $len = 0;
30
+ }else{
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+ s/[^A-Za-z]//g;
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+ $len+= length $_;
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+ }
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+ }
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+ print "$def\t$len\n" if $def;
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+ close FA;
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+ }
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+
@@ -0,0 +1,55 @@
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+ #!/usr/bin/env perl
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+ #
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+ # @author Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>
4
+ # @update Oct-13-2015
5
+ # @license artistic license 2.0
6
+ #
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+
8
+ use warnings;
9
+ use strict;
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+ use Symbol;
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+
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+ my ($file, $base, $outN) = @ARGV;
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+
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+ $outN ||= 12;
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+ ($file and $base) or die "
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+ Usage
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+ $0 in_file.fa out_base[ no_files]
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+
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+ in_file.fa Input file in FastA format.
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+ out_base Prefix for the name of the output files. It will
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+ be appended with .<i>.fa, where <i> is a consecutive
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+ number starting in 1.
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+ no_files Number of files to generate. By default: 12.
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+
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+ ";
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+
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+
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+ my @outSym = ();
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+ for my $i (1 .. $outN){
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+ $outSym[$i-1] = gensym;
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+ open $outSym[$i-1], ">", "$base.$i.fa" or
32
+ die "I can not create the file: $base.$i.fa: $!\n";
33
+ }
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+
35
+
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+ my($i, $seq) = (-1, '');
37
+ open FILE, "<", $file or die "I can not read the file: $file: $!\n";
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+ while(my $ln=<FILE>){
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+ next if $ln=~/^;/;
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+ if($ln =~ m/^>/){
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+ print { $outSym[$i % $outN] } $seq if $seq;
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+ $i++;
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+ $seq = '';
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+ }
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+ $seq.=$ln;
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+ }
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+ print { $outSym[$i % $outN] } $seq if $seq;
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+ close FILE;
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+
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+ for(my $j=0; $j<$outN; $j++){
51
+ close $outSym[$j];
52
+ }
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+
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+ print STDERR "Sequences: ".($i+1)."\nFiles: $outN\n";
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+
metadata CHANGED
@@ -1,109 +1,109 @@
1
1
  --- !ruby/object:Gem::Specification
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  name: miga-base
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3
  version: !ruby/object:Gem::Version
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- version: 0.3.0.6
4
+ version: 0.3.0.7
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5
  platform: ruby
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  authors:
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7
  - Luis M. Rodriguez-R
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  autorequire:
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  bindir: bin
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  cert_chain: []
11
- date: 2017-08-24 00:00:00.000000000 Z
11
+ date: 2017-08-25 00:00:00.000000000 Z
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  dependencies:
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  - !ruby/object:Gem::Dependency
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  name: rest-client
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  requirement: !ruby/object:Gem::Requirement
16
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  requirements:
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- - - "~>"
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+ - - ~>
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  - !ruby/object:Gem::Version
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  version: '1.7'
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20
  type: :runtime
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21
  prerelease: false
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  version_requirements: !ruby/object:Gem::Requirement
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23
  requirements:
24
- - - "~>"
24
+ - - ~>
25
25
  - !ruby/object:Gem::Version
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26
  version: '1.7'
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27
  - !ruby/object:Gem::Dependency
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  name: daemons
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  requirement: !ruby/object:Gem::Requirement
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  requirements:
31
- - - "~>"
31
+ - - ~>
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32
  - !ruby/object:Gem::Version
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33
  version: '1.2'
34
- - - ">="
34
+ - - '>='
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35
  - !ruby/object:Gem::Version
36
36
  version: 1.2.4
37
37
  type: :runtime
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  prerelease: false
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  version_requirements: !ruby/object:Gem::Requirement
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  requirements:
41
- - - "~>"
41
+ - - ~>
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  - !ruby/object:Gem::Version
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  version: '1.2'
44
- - - ">="
44
+ - - '>='
45
45
  - !ruby/object:Gem::Version
46
46
  version: 1.2.4
47
47
  - !ruby/object:Gem::Dependency
48
48
  name: json
49
49
  requirement: !ruby/object:Gem::Requirement
50
50
  requirements:
51
- - - ">"
51
+ - - '>'
52
52
  - !ruby/object:Gem::Version
53
53
  version: '1.8'
54
- - - "<"
54
+ - - <
55
55
  - !ruby/object:Gem::Version
56
56
  version: '3'
57
57
  type: :runtime
58
58
  prerelease: false
59
59
  version_requirements: !ruby/object:Gem::Requirement
60
60
  requirements:
61
- - - ">"
61
+ - - '>'
62
62
  - !ruby/object:Gem::Version
63
63
  version: '1.8'
64
- - - "<"
64
+ - - <
65
65
  - !ruby/object:Gem::Version
66
66
  version: '3'
67
67
  - !ruby/object:Gem::Dependency
68
68
  name: sqlite3
69
69
  requirement: !ruby/object:Gem::Requirement
70
70
  requirements:
71
- - - "~>"
71
+ - - ~>
72
72
  - !ruby/object:Gem::Version
73
73
  version: '1.3'
74
74
  type: :runtime
75
75
  prerelease: false
76
76
  version_requirements: !ruby/object:Gem::Requirement
77
77
  requirements:
78
- - - "~>"
78
+ - - ~>
79
79
  - !ruby/object:Gem::Version
80
80
  version: '1.3'
81
81
  - !ruby/object:Gem::Dependency
82
82
  name: rake
83
83
  requirement: !ruby/object:Gem::Requirement
84
84
  requirements:
85
- - - "~>"
85
+ - - ~>
86
86
  - !ruby/object:Gem::Version
87
87
  version: '11'
88
88
  type: :development
89
89
  prerelease: false
90
90
  version_requirements: !ruby/object:Gem::Requirement
91
91
  requirements:
92
- - - "~>"
92
+ - - ~>
93
93
  - !ruby/object:Gem::Version
94
94
  version: '11'
95
95
  - !ruby/object:Gem::Dependency
96
96
  name: test-unit
97
97
  requirement: !ruby/object:Gem::Requirement
98
98
  requirements:
99
- - - "~>"
99
+ - - ~>
100
100
  - !ruby/object:Gem::Version
101
101
  version: '3'
102
102
  type: :development
103
103
  prerelease: false
104
104
  version_requirements: !ruby/object:Gem::Requirement
105
105
  requirements:
106
- - - "~>"
106
+ - - ~>
107
107
  - !ruby/object:Gem::Version
108
108
  version: '3'
109
109
  description: Microbial Genomes Atlas
@@ -114,34 +114,6 @@ extensions: []
114
114
  extra_rdoc_files:
115
115
  - README.md
116
116
  files:
117
- - Gemfile
118
- - LICENSE
119
- - README.md
120
- - Rakefile
121
- - actions/about.rb
122
- - actions/add.rb
123
- - actions/add_result.rb
124
- - actions/daemon.rb
125
- - actions/date.rb
126
- - actions/files.rb
127
- - actions/find.rb
128
- - actions/get.rb
129
- - actions/init.rb
130
- - actions/ln.rb
131
- - actions/ls.rb
132
- - actions/new.rb
133
- - actions/plugins.rb
134
- - actions/rm.rb
135
- - actions/run.rb
136
- - actions/stats.rb
137
- - actions/tax_dist.rb
138
- - actions/tax_index.rb
139
- - actions/tax_set.rb
140
- - actions/tax_test.rb
141
- - bin/miga
142
- - lib/miga.rb
143
- - lib/miga/_data/aai-intax.tsv.gz
144
- - lib/miga/_data/aai-novel.tsv.gz
145
117
  - lib/miga/common.rb
146
118
  - lib/miga/daemon.rb
147
119
  - lib/miga/dataset.rb
@@ -155,6 +127,18 @@ files:
155
127
  - lib/miga/tax_index.rb
156
128
  - lib/miga/taxonomy.rb
157
129
  - lib/miga/version.rb
130
+ - lib/miga.rb
131
+ - test/common_test.rb
132
+ - test/daemon_test.rb
133
+ - test/dataset_test.rb
134
+ - test/metadata_test.rb
135
+ - test/project_test.rb
136
+ - test/remote_dataset_test.rb
137
+ - test/tax_index_test.rb
138
+ - test/taxonomy_test.rb
139
+ - test/test_helper.rb
140
+ - lib/miga/_data/aai-intax.tsv.gz
141
+ - lib/miga/_data/aai-novel.tsv.gz
158
142
  - scripts/_distances_functions.bash
159
143
  - scripts/_distances_noref_nomulti.bash
160
144
  - scripts/_distances_ref_nomulti.bash
@@ -178,23 +162,74 @@ files:
178
162
  - scripts/subclades.bash
179
163
  - scripts/trimmed_fasta.bash
180
164
  - scripts/trimmed_reads.bash
181
- - test/common_test.rb
182
- - test/daemon_test.rb
183
- - test/dataset_test.rb
184
- - test/metadata_test.rb
185
- - test/project_test.rb
186
- - test/remote_dataset_test.rb
187
- - test/tax_index_test.rb
188
- - test/taxonomy_test.rb
189
- - test/test_helper.rb
190
165
  - utils/adapters.fa
191
166
  - utils/core-pan-plot.R
167
+ - utils/enveomics/build_enveomics_r.bash
168
+ - utils/enveomics/enveomics.R/data/growth.curves.rda
169
+ - utils/enveomics/enveomics.R/data/phyla.counts.rda
170
+ - utils/enveomics/enveomics.R/DESCRIPTION
171
+ - utils/enveomics/enveomics.R/man/enve.__prune.iter.Rd
172
+ - utils/enveomics/enveomics.R/man/enve.__prune.reduce.Rd
173
+ - utils/enveomics/enveomics.R/man/enve.__tribs.Rd
174
+ - utils/enveomics/enveomics.R/man/enve.barplot.Rd
175
+ - utils/enveomics/enveomics.R/man/enve.cliopts.Rd
176
+ - utils/enveomics/enveomics.R/man/enve.col.alpha.Rd
177
+ - utils/enveomics/enveomics.R/man/enve.col2alpha.Rd
178
+ - utils/enveomics/enveomics.R/man/enve.df2dist.group.Rd
179
+ - utils/enveomics/enveomics.R/man/enve.df2dist.list.Rd
180
+ - utils/enveomics/enveomics.R/man/enve.df2dist.Rd
181
+ - utils/enveomics/enveomics.R/man/enve.GrowthCurve-class.Rd
182
+ - utils/enveomics/enveomics.R/man/enve.growthcurve.Rd
183
+ - utils/enveomics/enveomics.R/man/enve.prune.dist.Rd
184
+ - utils/enveomics/enveomics.R/man/enve.recplot.Rd
185
+ - utils/enveomics/enveomics.R/man/enve.recplot2-class.Rd
186
+ - utils/enveomics/enveomics.R/man/enve.recplot2.__counts.Rd
187
+ - utils/enveomics/enveomics.R/man/enve.recplot2.__findPeak.Rd
188
+ - utils/enveomics/enveomics.R/man/enve.recplot2.__findPeaks.Rd
189
+ - utils/enveomics/enveomics.R/man/enve.recplot2.__peakHist.Rd
190
+ - utils/enveomics/enveomics.R/man/enve.recplot2.__whichClosestPeak.Rd
191
+ - utils/enveomics/enveomics.R/man/enve.recplot2.changeCutoff.Rd
192
+ - utils/enveomics/enveomics.R/man/enve.recplot2.corePeak.Rd
193
+ - utils/enveomics/enveomics.R/man/enve.recplot2.extractWindows.Rd
194
+ - utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.Rd
195
+ - utils/enveomics/enveomics.R/man/enve.recplot2.peak-class.Rd
196
+ - utils/enveomics/enveomics.R/man/enve.recplot2.Rd
197
+ - utils/enveomics/enveomics.R/man/enve.TRIBS-class.Rd
198
+ - utils/enveomics/enveomics.R/man/enve.TRIBS.merge.Rd
199
+ - utils/enveomics/enveomics.R/man/enve.tribs.Rd
200
+ - utils/enveomics/enveomics.R/man/enve.tribs.test.Rd
201
+ - utils/enveomics/enveomics.R/man/enve.TRIBStest-class.Rd
202
+ - utils/enveomics/enveomics.R/man/enveomics.R-package.Rd
203
+ - utils/enveomics/enveomics.R/man/growth.curves.Rd
204
+ - utils/enveomics/enveomics.R/man/phyla.counts.Rd
205
+ - utils/enveomics/enveomics.R/man/plot.enve.GrowthCurve.Rd
206
+ - utils/enveomics/enveomics.R/man/plot.enve.recplot2.Rd
207
+ - utils/enveomics/enveomics.R/man/plot.enve.TRIBS.Rd
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  - Artistic-2.0
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461
460
  requirements:
462
- - - ">="
461
+ - - '>='
463
462
  - !ruby/object:Gem::Version
464
463
  version: '0'
465
464
  requirements: []
466
465
  rubyforge_project:
467
- rubygems_version: 2.6.11
466
+ rubygems_version: 2.0.14
468
467
  signing_key:
469
468
  specification_version: 4
470
469
  summary: MiGA
@@ -1 +0,0 @@
1
- utils/enveomics/Pipelines/assembly.pbs/../../Scripts/FastA.N50.pl
@@ -1 +0,0 @@
1
- utils/enveomics/Pipelines/assembly.pbs/../../Scripts/FastA.filterN.pl
@@ -1 +0,0 @@
1
- utils/enveomics/Pipelines/assembly.pbs/../../Scripts/FastA.length.pl
@@ -1 +0,0 @@
1
- utils/enveomics/Pipelines/blast.pbs/../../Scripts/FastA.split.pl
@@ -1 +0,0 @@
1
- utils/enveomics/Scripts/lib/../../enveomics.R