scbi_fastq 0.0.18 → 0.0.19

checksums.yaml

@@ -1,15 +1,7 @@
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data/.gitignore

@@ -0,0 +1,14 @@
+/.bundle/
+/.yardoc
+/Gemfile.lock
+/_yardoc/
+/coverage/
+/doc/
+/pkg/
+/spec/reports/
+/tmp/
+*.bundle
+*.so
+*.o
+*.a
+mkmf.log

data/Gemfile

@@ -0,0 +1,4 @@
+source 'https://rubygems.org'
+
+# Specify your gem's dependencies in scbi_fastq.gemspec
+gemspec

data/LICENSE.txt

@@ -0,0 +1,22 @@
+Copyright (c) 2014 dariogf
+
+MIT License
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/{README.rdoc → README.md}

@@ -105,27 +105,11 @@ scbi_fastq is a ruby gem to read/write FASTQ files (DNA/RNA sequences) with qual
 
 * gem install scbi_fastq
 
-== LICENSE:
-
-(The MIT License)
-
-Copyright (c) 2010 Dario Guerrero
-
-Permission is hereby granted, free of charge, to any person obtaining
-a copy of this software and associated documentation files (the
-'Software'), to deal in the Software without restriction, including
-without limitation the rights to use, copy, modify, merge, publish,
-distribute, sublicense, and/or sell copies of the Software, and to
-permit persons to whom the Software is furnished to do so, subject to
-the following conditions:
-
-The above copyright notice and this permission notice shall be
-included in all copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED 'AS IS', WITHOUT WARRANTY OF ANY KIND,
-EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
-MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
-IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
-CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
-TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
-SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+## Contributing
+
+1. Fork it ( https://github.com/[my-github-username]/scbi_fastq/fork )
+2. Create your feature branch (`git checkout -b my-new-feature`)
+3. Commit your changes (`git commit -am 'Add some feature'`)
+4. Push to the branch (`git push origin my-new-feature`)
+5. Create a new Pull Request
+

data/Rakefile

@@ -1,26 +1,8 @@
-require 'rubygems'
-gem 'hoe', '>= 2.1.0'
-require 'hoe'
-require 'fileutils'
-require './lib/scbi_fastq'
-
-Hoe.plugin :newgem
-# Hoe.plugin :website
-# Hoe.plugin :cucumberfeatures
-
-# Generate all the Rake tasks
-# Run 'rake -T' to see list of generated tasks (from gem root directory)
-$hoe = Hoe.spec 'scbi_fastq' do
-  self.developer 'Dario Guerrero', 'dariogf@scbi.uma.es'
-  self.post_install_message = 'PostInstall.txt' # TODO remove if post-install message not required
-  self.rubyforge_name       = self.name # TODO this is default value
-  # self.extra_deps         = [['activesupport','>= 2.0.2']]
-
-end
-
-require 'newgem/tasks'
-Dir['tasks/**/*.rake'].each { |t| load t }
-
-# TODO - want other tests/tasks run by default? Add them to the list
-# remove_task :default
-task :default => [:spec, :features, :redocs]
+require "bundler/gem_tasks"
+
+require 'rake/testtask'
+
+Rake::TestTask.new do |t|
+  t.libs << 'test'
+  t.pattern = "test/*_test.rb"
+end

data/lib/scbi_fastq.rb

@@ -1,7 +1,6 @@
-$:.unshift(File.dirname(__FILE__)) unless
-  $:.include?(File.dirname(__FILE__)) || $:.include?(File.expand_path(File.dirname(__FILE__)))
-
+require "scbi_fastq/version"
 require 'scbi_fastq/fastq_file'
+
 module ScbiFastq
-   VERSION = '0.0.18'
+  # Your code goes here...
 end

data/lib/scbi_fastq/fastq_file.rb

@@ -1,4 +1,5 @@
 require 'zlib'
+require 'scbi_multi_gz_reader'
 
 # add ord method to ruby 1.8
 if !String.instance_methods.include?(:ord)
@@ -22,7 +23,6 @@ class FastqFile
   #------------------------------------
   def initialize(fasta_file_name, mode='r', fastq_type = :sanger, qual_to_array=true, qual_to_phred=true)
 
-
      
     if mode.upcase.index('W.GZ')
       @fastq_file = Zlib::GzipWriter.open(fasta_file_name)
@@ -43,9 +43,10 @@ class FastqFile
         @fastq_file = fasta_file_name
       else
         begin
-          @fastq_file = Zlib::GzipReader.open(fasta_file_name)
+          #@fastq_file = Zlib::GzipReader.open(fasta_file_name)
+          @fastq_file = MultiGzReader.new(fasta_file_name)
           # puts "GZIP file detected"
-        rescue
+        rescue => e
           @fastq_file = File.open(fasta_file_name,'r')
           # puts "NORMAL file detected"
         end
@@ -158,7 +159,8 @@ class FastqFile
 
     @fastq_file.puts("@#{seq_name} #{comments}")
     @fastq_file.puts(seq_fasta)
-    @fastq_file.puts("+#{seq_name} #{comments}")
+    @fastq_file.puts("+")
+    #@fastq_file.puts("+#{seq_name} #{comments}")
 
     if seq_qual.is_a?(Array)
       @fastq_file.puts(seq_qual.map{|e| @from_phred.call(e)}.join)
@@ -178,7 +180,8 @@ class FastqFile
 
     res << ("@#{seq_name} #{comments}")
     res << (seq_fasta)
-    res << ("+#{seq_name} #{comments}")
+    res << ("+")
+    #res << ("+#{seq_name} #{comments}")
 
     if !seq_qual.empty?
       # if @qual_to_phred

data/lib/scbi_fastq/version.rb

@@ -0,0 +1,3 @@
+module ScbiFastq
+  VERSION = "0.0.19"
+end

data/scbi_fastq.gemspec

@@ -0,0 +1,24 @@
+# coding: utf-8
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'scbi_fastq/version'
+
+Gem::Specification.new do |spec|
+  spec.name          = "scbi_fastq"
+  spec.version       = ScbiFastq::VERSION
+  spec.authors       = ["dariogf"]
+  spec.email         = ["dariogf@scbi.uma.es"]
+  spec.summary       = %q{read/write FASTQ files}
+  spec.description   = %q{scbi_fastq is a ruby gem to read/write FASTQ files (DNA/RNA sequences) with qualities in a variety of formats (Sanger, Solexa, Ilumina).}
+  spec.homepage      = ""
+  spec.license       = "MIT"
+
+  spec.files         = `git ls-files -z`.split("\x0")
+  spec.executables   = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
+  spec.test_files    = spec.files.grep(%r{^(test|spec|features)/})
+  spec.require_paths = ["lib"]
+
+  spec.add_runtime_dependency "scbi_multi_gz_reader"
+  spec.add_development_dependency "bundler", "~> 1.7"
+  spec.add_development_dependency "rake", "~> 10.0"
+end

data/test/fq_all2std.pl

@@ -0,0 +1,194 @@
+#!/usr/local/bin/perl -w
+
+# Author: lh3
+
+use strict;
+use warnings;
+use Getopt::Std;
+
+my $usage = qq(
+Usage:   fq_all2std.pl <command> <in.txt>
+
+Command: scarf2std      Convert SCARF format to the standard/Sanger FASTQ
+         fqint2std      Convert FASTQ-int format to the standard/Sanger FASTQ
+         sol2std        Convert Solexa/Illumina FASTQ to the standard FASTQ
+         fa2std         Convert FASTA to the standard FASTQ
+         fq2fa          Convert various FASTQ-like format to FASTA
+         instruction    Explanation to different format
+         example        Show examples of various formats
+
+Note:    Read/quality sequences MUST be presented in one line.
+\n);
+
+die($usage) if (@ARGV < 1);
+
+# Solexa->Sanger quality conversion table
+my @conv_table;
+for (-64..64) {
+  $conv_table[$_+64] = chr(int(33 + 10*log(1+10**($_/10.0))/log(10)+.499));
+}
+
+# parsing command line
+my $cmd = shift;
+my %cmd_hash = (scarf2std=>\&scarf2std, fqint2std=>\&fqint2std, sol2std=>\&sol2std, fa2std=>\&fa2std,
+				fq2fa=>\&fq2fa, example=>\&example, instruction=>\&instruction);
+if (defined($cmd_hash{$cmd})) {
+  &{$cmd_hash{$cmd}};
+} else {
+  die("** Unrecognized command $cmd");
+}
+
+sub fa2std {
+  my %opts = (q=>25);
+  getopts('q:', \%opts);
+  my $q = chr($opts{q} + 33);
+  warn("-- The default quality is set to $opts{q}. Use '-q' at the command line to change the default.\n");
+  while (<>) {
+	if (/^>(\S+)/) {
+	  print "\@$1\n";
+	  $_ = <>;
+	  print "$_+\n", $q x (length($_)-1), "\n";
+	}
+  }
+}
+
+sub fq2fa {
+  while (<>) {
+	if (/^@(\S+)/) {
+	  print ">$1\n";
+	  $_ = <>; print;
+	  <>; <>;
+	}
+  }
+}
+
+sub scarf2std {
+  while (<>) {
+	my @t = split(':', $_);
+	my $name = join('_', @t[0..4]);
+	print "\@$name\n$t[5]\n+\n";
+	my $qual = '';
+	@t = split(/\s/, $t[6]);
+	$qual .= $conv_table[$_+64] for (@t);
+	print "$qual\n";
+  }
+}
+
+sub fqint2std {
+  while (<>) {
+	if (/^@/) {
+	  print;
+	  $_ = <>; print; $_ = <>; $_ = <>;
+	  my @t = split;
+	  my $qual = '';
+	  $qual .= $conv_table[$_+64] for (@t);
+	  print "+\n$qual\n";
+	}
+  }
+}
+
+sub sol2std {
+  my $max = 0;
+  while (<>) {
+	if (/^@/) {
+	  print;
+	  $_ = <>; print; $_ = <>; $_ = <>;
+	  my @t = split('', $_);
+	  my $qual = '';
+	  $qual .= $conv_table[ord($_)] for (@t);
+	  print "+\n$qual\n";
+	}
+  }
+}
+
+sub instruction {
+
+  print "
+FASTQ format is first used in the Sanger Institute, and therefore
+we take the Sanger specification as the standard FASTQ. Although
+Solexa/Illumina reads file looks pretty much like the standard
+FASTQ, they are different in that the qualities are scaled
+differently. In the quality string, if you can see a character
+with its ASCII code higher than 90, probably your file is in the
+Solexa/Illumina format.
+
+Sometimes we also use an integer, instead of a single character,
+to explicitly show the qualities. In that case, negative
+qualities indicates that Solexa/Illumina qualities are used.
+
+";
+
+}
+
+sub example {
+  my $exam_scarf = '
+USI-EAS50_1:4:2:710:120:GTCAAAGTAATAATAGGAGATTTGAGCTATTT:23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 19 23 23 23 18 23 23 23
+USI-EAS50_1:4:2:690:87:GTTTTTTTTTTTCTTTCCATTAATTTCCCTTT:23 23 23 23 23 23 23 23 23 23 23 23 12 23 23 23 23 23 16 23 23 9 18 23 23 23 12 23 18 23 23 23
+USI-EAS50_1:4:2:709:32:GAGAAGTCAAACCTGTGTTAGAAATTTTATAC:23 23 23 23 23 23 23 23 20 23 23 23 23 23 23 23 23 23 23 23 23 12 23 18 23 23 23 23 23 23 23 23
+USI-EAS50_1:4:2:886:890:GCTTATTTAAAAATTTACTTGGGGTTGTCTTT:23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23
+USI-EAS50_1:4:2:682:91:GGGTTTCTAGACTAAAGGGATTTAACAAGTTT:23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 20 23 23 23 23 23 23 23 23 23 23 23 18 23 23 23 23
+USI-EAS50_1:4:2:663:928:GAATTTGTTTGAAGAGTGTCATGGTCAGATCT:23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23
+';
+
+  my $exam_fqint = '
+@4_1_912_360
+AAGGGGCTAGAGAAACACGTAATGAAGGGAGGACTC
++4_1_912_360
+40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 21 40 40 40 40 40 40 40 40 40 26 40 40 14 39 40 40
+@4_1_54_483
+TAATAAATGTGCTTCCTTGATGCATGTGCTATGATT
++4_1_54_483
+40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 16 40 40 40 28 40 40 40 40 40 40 16 40 40 5 40 40
+@4_1_537_334
+ATTGATGATGCTGTGCACCTAGCAAGAAGTTGCATA
++4_1_537_334
+40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 21 29 40 40 33 40 40 33 40 40 33 31 40 40 40 40 18 26 40 -2
+@4_1_920_361
+AACGGCACAATCCAGGTTGATGCCTACGGCGGGTAC
++4_1_920_361
+40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 40 40 40 40 40 40 40 40 31 40 40 40 40 40 40 15 5 -1 3
+@4_1_784_155
+AATGCATGCTTCGAATGGCATTCTCTTCAATCACGA
++4_1_784_155
+40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 31 40 40 40 40 40
+@4_1_595_150
+AAAGACGTGGCCAGATGGGTGGCCAAGTGCCCGACT
++4_1_595_150
+40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 30 40 40 40 40 40 40 40 40 40 20 40 40 40 40 40 14 40 40
+';
+
+  my $exam_sol = '
+@SLXA-B3_649_FC8437_R1_1_1_610_79
+GATGTGCAATACCTTTGTAGAGGAA
++SLXA-B3_649_FC8437_R1_1_1_610_79
+YYYYYYYYYYYYYYYYYYWYWYYSU
+@SLXA-B3_649_FC8437_R1_1_1_397_389
+GGTTTGAGAAAGAGAAATGAGATAA
++SLXA-B3_649_FC8437_R1_1_1_397_389
+YYYYYYYYYWYYYYWWYYYWYWYWW
+@SLXA-B3_649_FC8437_R1_1_1_850_123
+GAGGGTGTTGATCATGATGATGGCG
++SLXA-B3_649_FC8437_R1_1_1_850_123
+YYYYYYYYYYYYYWYYWYYSYYYSY
+@SLXA-B3_649_FC8437_R1_1_1_362_549
+GGAAACAAAGTTTTTCTCAACATAG
++SLXA-B3_649_FC8437_R1_1_1_362_549
+YYYYYYYYYYYYYYYYYYWWWWYWY
+@SLXA-B3_649_FC8437_R1_1_1_183_714
+GTATTATTTAATGGCATACACTCAA
++SLXA-B3_649_FC8437_R1_1_1_183_714
+YYYYYYYYYYWYYYYWYWWUWWWQQ
+';
+
+  print qq(
+solexa
+======
+$exam_sol
+scarf
+=====
+$exam_scarf
+fqint
+=====
+$exam_fqint
+);
+}

data/test/gz.rb

@@ -0,0 +1,11 @@
+require '../lib/scbi_fastq/multi_gz_reader'
+
+ file=MultiGzReader.new(File.join(File.dirname(__FILE__),'minitest.fastq.gz'))
+
+    loop do
+      res=file.readline
+      puts "LINE: #{res}"
+      break if res.nil?
+    end
+
+    file.close

data/test/prueba.rb

@@ -0,0 +1,8 @@
+require File.dirname(__FILE__) + '/test_helper.rb'
+
+fqr=FastqFile.new('./sanger.fastq.gz')
+
+fqr.each do |n,f,q|
+  puts n  
+end
+fqr.close