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 +4 -4
- data/lib/miga/project.rb +4 -3
- data/lib/miga/version.rb +2 -2
- data/utils/enveomics/Pipelines/assembly.pbs/FastA.N50.pl +56 -0
- data/utils/enveomics/Pipelines/assembly.pbs/FastA.filterN.pl +60 -0
- data/utils/enveomics/Pipelines/assembly.pbs/FastA.length.pl +38 -0
- data/utils/enveomics/Pipelines/blast.pbs/FastA.split.pl +55 -0
- metadata +160 -161
- data/utils/enveomics/Pipelines/assembly.pbs/FastA.N50.pl +0 -1
- data/utils/enveomics/Pipelines/assembly.pbs/FastA.filterN.pl +0 -1
- data/utils/enveomics/Pipelines/assembly.pbs/FastA.length.pl +0 -1
- data/utils/enveomics/Pipelines/blast.pbs/FastA.split.pl +0 -1
- data/utils/enveomics/Scripts/lib/enveomics.R +0 -1
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
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---
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SHA1:
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-
metadata.gz:
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-
data.tar.gz:
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+
metadata.gz: 4132f066f463f3967517e7e278b765087a22bb89
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data.tar.gz: 78fcfd7accea31d041991f26944d701cc6b31fef
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: b7446a3f81368c04f4e8cdec66abe28eb7eeb0c9f00d046dee1b4882007c8f4f2325052f466069407a17a0d65b1e6b1cc274fa10f2a3c5dabf7684a3f34e6852
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data.tar.gz: 1c47807eb8e3a97b2cd464495a0fd022f6c8f1aa86bfd8ed6dc018d376f63994dded3616467df4528b9286a057f0ac4e219313f76fa03542ad143925403c877d
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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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-
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-
return
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-
r =
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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
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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,
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+
VERSION = [0.3, 0, 7]
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##
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# Nickname for the current major.minor version.
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@@ -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,
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VERSION_DATE = Date.new(2017, 8, 25)
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##
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# Reference of MiGA.
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@@ -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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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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Usage:
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$0 seqs.fa[ minlen[ **]]
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seqs.fa A FastA file containing the sequences.
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minlen (optional) The minimum length to take into consideration.
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By default: 0.
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** Value N** to calculate. By default: 50 (N50).
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";
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$minlen ||= 0;
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$n__ ||= 50;
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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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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: $tot\n";
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@@ -0,0 +1,60 @@
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#!/usr/bin/env perl
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#
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# @author Luis M. Rodriguez-R
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# @update Oct-07-2015
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# @license artistic license 2.0
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#
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use warnings;
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use strict;
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my($file, $content, $stretch) = @ARGV;
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$file or die <<HELP
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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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$0 sequences.fa [content [stretch]] > filtered.fa
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Where:
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sequences.fa Input file in FastA format
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content A number between 0 and 1 indicating the maximum proportion of Ns
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(1 to turn off, 0.5 by default)
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stretch A number indicating the maximum number of consecutive identical
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nucleotides allowed (0 to turn off, 100 by default)
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filtered.fa Filtered set of sequences.
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HELP
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;
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($content ||= 0.5)+=0;
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($stretch ||= 100)+=0;
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my $good = 0;
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my $N = 0;
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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: $good\n";
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}
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+
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+
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@@ -0,0 +1,38 @@
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#!/usr/bin/env perl
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#
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# @author Luis M Rodriguez-R
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# @update Oct-07-2015
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# @license artistic license 2.0
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#
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use warnings;
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use strict;
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+
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$#ARGV>=0 or die "
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Usage:
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$0 seqs.fa... > length.txt
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seqs.fa One or more FastA files.
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length.txt A table with the lengths of the sequences.
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+
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";
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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;
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}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 $def;
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close FA;
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}
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+
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@@ -0,0 +1,55 @@
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1
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#!/usr/bin/env perl
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2
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#
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# @author Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>
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4
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# @update Oct-13-2015
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# @license artistic license 2.0
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#
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+
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use warnings;
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+
use strict;
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10
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+
use Symbol;
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+
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my ($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){
|
30
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+
$outSym[$i-1] = gensym;
|
31
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+
open $outSym[$i-1], ">", "$base.$i.fa" or
|
32
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die "I can not create the file: $base.$i.fa: $!\n";
|
33
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+
}
|
34
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+
|
35
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+
|
36
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+
my($i, $seq) = (-1, '');
|
37
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+
open FILE, "<", $file or die "I can not read the file: $file: $!\n";
|
38
|
+
while(my $ln=<FILE>){
|
39
|
+
next if $ln=~/^;/;
|
40
|
+
if($ln =~ m/^>/){
|
41
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+
print { $outSym[$i % $outN] } $seq if $seq;
|
42
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+
$i++;
|
43
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+
$seq = '';
|
44
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+
}
|
45
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+
$seq.=$ln;
|
46
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+
}
|
47
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+
print { $outSym[$i % $outN] } $seq if $seq;
|
48
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+
close FILE;
|
49
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+
|
50
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+
for(my $j=0; $j<$outN; $j++){
|
51
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+
close $outSym[$j];
|
52
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+
}
|
53
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+
|
54
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+
print STDERR "Sequences: ".($i+1)."\nFiles: $outN\n";
|
55
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+
|
metadata
CHANGED
@@ -1,109 +1,109 @@
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1
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--- !ruby/object:Gem::Specification
|
2
2
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name: miga-base
|
3
3
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version: !ruby/object:Gem::Version
|
4
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-
version: 0.3.0.
|
4
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+
version: 0.3.0.7
|
5
5
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platform: ruby
|
6
6
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authors:
|
7
7
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- Luis M. Rodriguez-R
|
8
8
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autorequire:
|
9
9
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bindir: bin
|
10
10
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cert_chain: []
|
11
|
-
date: 2017-08-
|
11
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+
date: 2017-08-25 00:00:00.000000000 Z
|
12
12
|
dependencies:
|
13
13
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- !ruby/object:Gem::Dependency
|
14
14
|
name: rest-client
|
15
15
|
requirement: !ruby/object:Gem::Requirement
|
16
16
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requirements:
|
17
|
-
- -
|
17
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+
- - ~>
|
18
18
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- !ruby/object:Gem::Version
|
19
19
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version: '1.7'
|
20
20
|
type: :runtime
|
21
21
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prerelease: false
|
22
22
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version_requirements: !ruby/object:Gem::Requirement
|
23
23
|
requirements:
|
24
|
-
- -
|
24
|
+
- - ~>
|
25
25
|
- !ruby/object:Gem::Version
|
26
26
|
version: '1.7'
|
27
27
|
- !ruby/object:Gem::Dependency
|
28
28
|
name: daemons
|
29
29
|
requirement: !ruby/object:Gem::Requirement
|
30
30
|
requirements:
|
31
|
-
- -
|
31
|
+
- - ~>
|
32
32
|
- !ruby/object:Gem::Version
|
33
33
|
version: '1.2'
|
34
|
-
- -
|
34
|
+
- - '>='
|
35
35
|
- !ruby/object:Gem::Version
|
36
36
|
version: 1.2.4
|
37
37
|
type: :runtime
|
38
38
|
prerelease: false
|
39
39
|
version_requirements: !ruby/object:Gem::Requirement
|
40
40
|
requirements:
|
41
|
-
- -
|
41
|
+
- - ~>
|
42
42
|
- !ruby/object:Gem::Version
|
43
43
|
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
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