seqtrimnext 2.0.59 → 2.0.60

data/Manifest.txt

@@ -1,125 +0,0 @@
-bin/create_graphs.rb
-bin/extract_seqs.rb
-bin/extract_seqs_from_fasta.rb
-bin/extract_seqs_from_fastq.rb
-bin/fasta2fastq.rb
-bin/fastq2fasta.rb
-bin/filter_database.rb
-bin/gen_qual.rb
-bin/get_seq.rb
-bin/group_by_range.rb
-bin/join_big_illumina_paired.sh
-bin/join_ilumina_paired.rb
-bin/parse_amplicons.rb
-bin/parse_json_results.rb
-bin/parse_params.rb
-bin/resume_clusters.rb
-bin/resume_rejected.rb
-bin/reverse_paired.rb
-bin/seqtrimnext
-bin/split_fastq.rb
-bin/split_fasta.rb
-bin/split_ilumina_paired.rb
-bin/split_paired.rb
-History.txt
-lib/seqtrimnext/actions/action_ab_adapter.rb
-lib/seqtrimnext/actions/action_ab_far_adapter.rb
-lib/seqtrimnext/actions/action_ab_left_adapter.rb
-lib/seqtrimnext/actions/action_sanger_left_adapter.rb
-lib/seqtrimnext/actions/action_sanger_right_adapter.rb
-lib/seqtrimnext/actions/action_user_contaminant.rb
-lib/seqtrimnext/actions/action_empty_insert.rb
-lib/seqtrimnext/actions/action_ignore_repeated.rb
-lib/seqtrimnext/actions/action_indetermination.rb
-lib/seqtrimnext/actions/action_induced_low_complexity.rb
-lib/seqtrimnext/actions/action_insert.rb
-lib/seqtrimnext/actions/action_is_contaminated.rb
-lib/seqtrimnext/actions/action_key.rb
-lib/seqtrimnext/actions/action_left_adapter.rb
-lib/seqtrimnext/actions/action_left_primer.rb
-lib/seqtrimnext/actions/action_linker.rb
-lib/seqtrimnext/actions/action_low_complexity.rb
-lib/seqtrimnext/actions/action_low_high_size.rb
-lib/seqtrimnext/actions/action_low_quality.rb
-lib/seqtrimnext/actions/action_mid.rb
-lib/seqtrimnext/actions/action_middle_adapter.rb
-lib/seqtrimnext/actions/action_multiple_linker.rb
-lib/seqtrimnext/actions/action_paired_reads.rb
-lib/seqtrimnext/actions/action_poly_a.rb
-lib/seqtrimnext/actions/action_poly_t.rb
-lib/seqtrimnext/actions/action_rem_adit_artifacts.rb
-lib/seqtrimnext/actions/action_right_adapter.rb
-lib/seqtrimnext/actions/action_right_primer.rb
-lib/seqtrimnext/actions/action_short_insert.rb
-lib/seqtrimnext/actions/action_unexpected_poly_t.rb
-lib/seqtrimnext/actions/action_unexpected_vector.rb
-lib/seqtrimnext/actions/action_vectors.rb
-lib/seqtrimnext/actions/seqtrim_action.rb
-lib/seqtrimnext/classes/action_manager.rb
-lib/seqtrimnext/classes/em_classes/seqtrim_work_manager.rb
-lib/seqtrimnext/classes/em_classes/seqtrim_worker.rb
-lib/seqtrimnext/classes/extract_stats.rb
-lib/seqtrimnext/classes/gnu_plot_graph.rb
-lib/seqtrimnext/classes/graph_stats.rb
-lib/seqtrimnext/classes/install_database.rb
-lib/seqtrimnext/classes/install_requirements.rb
-lib/seqtrimnext/classes/list_db.rb
-lib/seqtrimnext/classes/make_blast_db.rb
-lib/seqtrimnext/classes/one_blast.rb
-lib/seqtrimnext/classes/params.rb
-lib/seqtrimnext/classes/piro.rb
-lib/seqtrimnext/classes/plugin_manager.rb
-lib/seqtrimnext/classes/scan_for_restr_site.rb
-lib/seqtrimnext/classes/scbi_stats.rb
-lib/seqtrimnext/classes/seqtrim.rb
-lib/seqtrimnext/classes/sequence.rb
-lib/seqtrimnext/classes/sequence_group.rb
-lib/seqtrimnext/classes/sequence_with_action.rb
-lib/seqtrimnext/plugins/plugin.rb
-lib/seqtrimnext/plugins/plugin_ab_adapters.rb
-lib/seqtrimnext/plugins/plugin_sanger_adapters.rb
-lib/seqtrimnext/plugins/plugin_adapters.rb
-lib/seqtrimnext/plugins/plugin_amplicons.rb
-lib/seqtrimnext/plugins/plugin_contaminants.rb
-lib/seqtrimnext/plugins/plugin_user_contaminants.rb
-lib/seqtrimnext/plugins/plugin_extract_inserts.rb
-lib/seqtrimnext/plugins/plugin_find_poly_at.rb
-lib/seqtrimnext/plugins/plugin_ignore_repeated.rb
-lib/seqtrimnext/plugins/plugin_indeterminations.rb
-lib/seqtrimnext/plugins/plugin_key.rb
-lib/seqtrimnext/plugins/plugin_linker.rb
-lib/seqtrimnext/plugins/plugin_low_complexity.rb
-lib/seqtrimnext/plugins/plugin_low_high_size.rb
-lib/seqtrimnext/plugins/plugin_low_quality.rb
-lib/seqtrimnext/plugins/plugin_mids.rb
-lib/seqtrimnext/plugins/plugin_short_insert.rb
-lib/seqtrimnext/plugins/plugin_vectors.rb
-lib/seqtrimnext/templates/amplicons.txt
-lib/seqtrimnext/templates/sanger.txt
-lib/seqtrimnext/templates/only_quality.txt
-lib/seqtrimnext/templates/genomics_454.txt
-lib/seqtrimnext/templates/genomics_454_with_paired.txt
-lib/seqtrimnext/templates/genomics_short_reads.txt
-lib/seqtrimnext/templates/genomics_short_reads_2.txt
-lib/seqtrimnext/templates/transcriptomics_454.txt
-lib/seqtrimnext/templates/transcriptomics_short_reads.txt
-lib/seqtrimnext/templates/transcriptomics_454_plants.txt
-lib/seqtrimnext/utils/extract_samples.rb
-lib/seqtrimnext/utils/fasta2xml.rb
-lib/seqtrimnext/utils/global_match.rb
-lib/seqtrimnext/utils/hash_stats.rb
-lib/seqtrimnext/utils/json_utils.rb
-lib/seqtrimnext/utils/load_fasta_names_in_hash.rb
-lib/seqtrimnext/utils/load_qual_in_hash.rb
-lib/seqtrimnext/utils/recover_mid.rb
-lib/seqtrimnext/utils/string_utils.rb
-lib/seqtrimnext.rb
-Manifest.txt
-PostInstall.txt
-Rakefile
-README.rdoc
-script/console
-script/destroy
-script/generate
-test/test_helper.rb
-test/test_seqtrimnext.rb

data/PostInstall.txt

@@ -1,7 +0,0 @@
-For more information on seqtrimnext, see http://www.scbi.uma.es
-
-Remember to install the following external prerequisites if you don't have them already installed.
-
-If you need to install core databases, issue the following command:
-
-seqtrimnext -i core

data/script/console

@@ -1,10 +0,0 @@
-#!/usr/bin/env ruby
-# File: script/console
-irb = RUBY_PLATFORM =~ /(:?mswin|mingw)/ ? 'irb.bat' : 'irb'
-
-libs =  " -r irb/completion"
-# Perhaps use a console_lib to store any extra methods I may want available in the cosole
-# libs << " -r #{File.dirname(__FILE__) + '/../lib/console_lib/console_logger.rb'}"
-libs <<  " -r #{File.dirname(__FILE__) + '/../lib/seqtrimnext.rb'}"
-puts "Loading seqtrimnext gem"
-exec "#{irb} #{libs} --simple-prompt"

data/script/destroy

@@ -1,14 +0,0 @@
-#!/usr/bin/env ruby
-APP_ROOT = File.expand_path(File.join(File.dirname(__FILE__), '..'))
-
-begin
-  require 'rubigen'
-rescue LoadError
-  require 'rubygems'
-  require 'rubigen'
-end
-require 'rubigen/scripts/destroy'
-
-ARGV.shift if ['--help', '-h'].include?(ARGV[0])
-RubiGen::Base.use_component_sources! [:rubygems, :newgem, :newgem_theme, :test_unit]
-RubiGen::Scripts::Destroy.new.run(ARGV)

data/script/generate

@@ -1,14 +0,0 @@
-#!/usr/bin/env ruby
-APP_ROOT = File.expand_path(File.join(File.dirname(__FILE__), '..'))
-
-begin
-  require 'rubigen'
-rescue LoadError
-  require 'rubygems'
-  require 'rubigen'
-end
-require 'rubigen/scripts/generate'
-
-ARGV.shift if ['--help', '-h'].include?(ARGV[0])
-RubiGen::Base.use_component_sources! [:rubygems, :newgem, :newgem_theme, :test_unit]
-RubiGen::Scripts::Generate.new.run(ARGV)

data/test/test_helper.rb

@@ -1,3 +0,0 @@
-require 'stringio'
-require 'test/unit'
-require File.dirname(__FILE__) + '/../lib/seqtrimnext'

data/test/test_seqtrimnext.rb

@@ -1,11 +0,0 @@
-require File.dirname(__FILE__) + '/test_helper.rb'
-
-class TestSeqtrimnext < Test::Unit::TestCase
-
-  def setup
-  end
-  
-  def test_truth
-    assert true
-  end
-end