bio-blast-xmlparser 0.0.0

checksums.yaml

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data/.gitignore

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+/.bundle/
+/.yardoc
+/Gemfile.lock
+/_yardoc/
+/coverage/
+/rdoc/
+/pkg/
+/spec/reports/
+/tmp/
+*~

data/BSDL

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+Copyright (C) 1993-2013 Yukihiro Matsumoto. All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions
+are met:
+1. Redistributions of source code must retain the above copyright
+notice, this list of conditions and the following disclaimer.
+2. Redistributions in binary form must reproduce the above copyright
+notice, this list of conditions and the following disclaimer in the
+documentation and/or other materials provided with the distribution.
+
+THIS SOFTWARE IS PROVIDED BY THE AUTHOR AND CONTRIBUTORS ``AS IS'' AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ARE DISCLAIMED.  IN NO EVENT SHALL THE AUTHOR OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS
+OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+SUCH DAMAGE.

data/COPYING

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+bio-blast-xmlparser is copyrighted free software by BioRuby Project <staff@bioruby.org>.
+You can redistribute it and/or modify it under either the terms of the
+2-clause BSDL (see the file BSDL), or the conditions below:
+
+  1. You may make and give away verbatim copies of the source form of the
+     software without restriction, provided that you duplicate all of the
+     original copyright notices and associated disclaimers.
+
+  2. You may modify your copy of the software in any way, provided that
+     you do at least ONE of the following:
+
+       a) place your modifications in the Public Domain or otherwise
+          make them Freely Available, such as by posting said
+	  modifications to Usenet or an equivalent medium, or by allowing
+	  the author to include your modifications in the software.
+
+       b) use the modified software only within your corporation or
+          organization.
+
+       c) give non-standard binaries non-standard names, with
+          instructions on where to get the original software distribution.
+
+       d) make other distribution arrangements with the author.
+
+  3. You may distribute the software in object code or binary form,
+     provided that you do at least ONE of the following:
+
+       a) distribute the binaries and library files of the software,
+	  together with instructions (in the manual page or equivalent)
+	  on where to get the original distribution.
+
+       b) accompany the distribution with the machine-readable source of
+	  the software.
+
+       c) give non-standard binaries non-standard names, with
+          instructions on where to get the original software distribution.
+
+       d) make other distribution arrangements with the author.
+
+  4. You may modify and include the part of the software into any other
+     software (possibly commercial).  But some files in the distribution
+     are not written by the author, so that they are not under these terms.
+
+     For the list of those files and their copying conditions, see the
+     file LEGAL.
+
+  5. The scripts and library files supplied as input to or produced as 
+     output from the software do not automatically fall under the
+     copyright of the software, but belong to whomever generated them, 
+     and may be sold commercially, and may be aggregated with this
+     software.
+
+  6. THIS SOFTWARE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR
+     IMPLIED WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED
+     WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+     PURPOSE.

data/COPYING.ja

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+本プログラムはフリーソフトウェアです．2-clause BSDL
+または以下に示す条件で本プログラムを再配布できます
+2-clause BSDLについてはBSDLファイルを参照して下さい．
+
+  1. 複製は制限なく自由です．
+
+  2. 以下の条件のいずれかを満たす時に本プログラムのソースを
+     自由に変更できます．
+
+     (a) ネットニューズにポストしたり，作者に変更を送付する
+         などの方法で，変更を公開する．
+
+     (b) 変更した本プログラムを自分の所属する組織内部だけで
+         使う．
+
+     (c) 変更点を明示したうえ，ソフトウェアの名前を変更する．
+         そのソフトウェアを配布する時には変更前の本プログラ
+         ムも同時に配布する．または変更前の本プログラムのソー
+         スの入手法を明示する．
+
+     (d) その他の変更条件を作者と合意する．
+
+  3. 以下の条件のいずれかを満たす時に本プログラムをコンパイ
+     ルしたオブジェクトコードや実行形式でも配布できます．
+
+     (a) バイナリを受け取った人がソースを入手できるように，
+         ソースの入手法を明示する．
+
+     (b) 機械可読なソースコードを添付する．
+
+     (c) 変更を行ったバイナリは名前を変更したうえ，オリジナ
+         ルのソースコードの入手法を明示する．
+
+     (d) その他の配布条件を作者と合意する．
+
+  4. 他のプログラムへの引用はいかなる目的であれ自由です．た
+     だし，本プログラムに含まれる他の作者によるコードは，そ
+     れぞれの作者の意向による制限が加えられる場合があります．
+
+     それらファイルの一覧とそれぞれの配布条件などに付いては
+     LEGALファイルを参照してください．
+
+  5. 本プログラムへの入力となるスクリプトおよび，本プログラ
+     ムからの出力の権利は本プログラムの作者ではなく，それぞ
+     れの入出力を生成した人に属します．また，本プログラムに
+     組み込まれるための拡張ライブラリについても同様です．
+
+  6. 本プログラムは無保証です．作者は本プログラムをサポート
+     する意志はありますが，プログラム自身のバグあるいは本プ
+     ログラムの実行などから発生するいかなる損害に対しても責
+     任を持ちません．

data/Gemfile

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+source "https://rubygems.org"
+
+git_source(:github) {|repo_name| "https://github.com/#{repo_name}" }
+
+# Specify your gem's dependencies in bio-plugin-blast-xmlparser.gemspec
+gemspec

data/LEGAL

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+LEGAL NOTICE INFORMATION
+------------------------
+
+All the files in this distribution are covered under either the Ruby's
+license (see the file COPYING) or public-domain except some files
+mentioned below.
+
+(no files)

data/README.md

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+# BioRuby BLAST XMLParser Plugin
+
+[![Build Status](https://secure.travis-ci.org/bioruby/bio-blast-xmlparser.png)](http://travis-ci.org/bioruby/bio-blast-xmlparser)
+
+bio-blast-xmlparser is a plugin of BioRuby, providing fast BLAST
+XML result parser by using XMLParser native extension.
+The code was formerly a part of the [BioRuby](http://bioruby.org/)
+core ("bio" gem), and because of the dependency to the native XMLParser
+extension, it was moved to this gem.
+
+This gem is also developed as part of an effort to
+[modularize](http://bioruby.open-bio.org/wiki/Plugins) BioRuby.
+Many more plugins are available at [biogems.info](http://www.biogems.info/).
+
+
+## Requirements
+
+bio-blast-xmlparser uses `xmplarser` gem that needs
+[expat XML Parser Toolkit]{http://www.jclark.com/xml/expat.html}
+installed on the system.
+
+On Debian/Ubuntu:
+
+    # apt-get install libexpat-dev
+
+On RedHat/CentOS:
+
+    # yum install expat-devel
+
+
+## Installation
+
+Add this line to your application's Gemfile:
+
+```ruby
+gem 'bio-blast-xmlparser'
+```
+
+And then execute:
+
+    $ bundle
+
+Or install it yourself as:
+
+    $ gem install bio-blast-xmlparser
+
+## Usage
+
+The existance of the gem is automatically detected by BioRuby core components.
+
+## Development
+
+To install this gem onto your local machine, run `bundle exec rake install`.
+To release a new version, update the version number in `version.rb`,
+and then run `bundle exec rake release`, which will create a git tag
+for the version, push git commits and tags, and push the `.gem` file
+to [rubygems.org](https://rubygems.org).
+
+## Contributing
+
+Bug reports and pull requests are welcome on GitHub at
+https://github.com/bioruby/bioruby-blast-xmlparser
+
+## Cite
+
+If you use this software, please cite one of
+
+* [BioRuby: bioinformatics software for the Ruby programming language](http://dx.doi.org/10.1093/bioinformatics/btq475)
+* [Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics](http://dx.doi.org/10.1093/bioinformatics/bts080)
+

data/Rakefile

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+require "bundler/gem_tasks"
+require 'rdoc/task'
+require 'rake/testtask'
+
+task :default => :test
+
+Rake::TestTask.new do |t|
+  t.test_files = FileList["test/**/test_*.rb"]
+end
+
+Rake::RDocTask.new do |r|
+  r.rdoc_dir = "rdoc"
+  r.rdoc_files.include("README.md",
+                       "COPYING", "COPYING.ja", "BSDL", "LEGAL",
+                       "lib/**/*.rb")
+  r.main = "README.md"
+  r.options << '--title' << 'BioRuby BLAST XMLParser Plugin API documentation'
+  r.options << '--line-numbers'
+end
+

data/bio-blast-xmlparser.gemspec

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+# coding: utf-8
+lib = File.expand_path("../lib", __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require "bio-blast-xmlparser/version"
+
+Gem::Specification.new do |spec|
+  spec.name          = "bio-blast-xmlparser"
+  spec.version       = Bio::BlastXMLParser::VERSION
+  spec.authors       = ["BioRuby project"]
+  spec.email         = ["staff@bioruby.org"]
+
+  spec.summary       = %q{BioRuby BLAST XMLParser plugin}
+  spec.description   = %q{BioRuby BLAST XMLParser plugin: a plugin of BioRuby BLAST XML result parser by using the XMLParser extension. This was formerly a part of the BioRuby core ("bio" gem) and split to this gem because of the external XMLParser dependency.}
+  spec.homepage      = "https://github.com/bioruby/bioruby-blast-xmlparser"
+
+  spec.files         = `git ls-files -z`.split("\x0").reject do |f|
+    f.match(%r{^(test|spec|features)/})
+  end
+  spec.bindir        = "bin"
+  spec.executables   = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
+  spec.require_paths = ["lib"]
+
+  spec.add_runtime_dependency "bio", ">= 2.0.0"
+  spec.add_runtime_dependency "xmlparser", "~> 0.7.2"
+
+  spec.add_development_dependency "bundler", ">= 1.15"
+  spec.add_development_dependency "rake", ">= 10.0"
+  spec.add_development_dependency "rdoc", ">= 5"
+  spec.add_development_dependency "test-unit", "~> 3"
+end

data/lib/bio-blast-xmlparser.rb

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+#
+
+require "bio" unless defined? Bio
+require_relative "bio/appl/blast/xmlparser"
+

data/lib/bio-blast-xmlparser/version.rb

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+module Bio
+  module BlastXMLParser
+    VERSION = "0.0.0".freeze
+  end
+end

data/lib/bio/appl/blast/xmlparser.rb

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+#
+# = bio/appl/blast/xmlparser.rb - BLAST XML output (-m 7) parser by XMLParser
+# 
+# Copyright::  Copyright (C) 2001 
+#              Mitsuteru C. Nakao <n@bioruby.org>
+# Copyright::  Copyright (C) 2003 
+#              Toshiaki Katayama <k@bioruby.org>
+# License::    The Ruby License
+#
+# $Id:$
+#
+# == Description
+# 
+# A parser for blast XML report (format 7) based on the XMLParser.
+# This file is automatically loaded by bio/appl/blast/report.rb if
+# the XMLParser installed.
+#
+# BioRuby provides two implements of the paser for the blast XML format report
+# (format 7) based on the XMLParser and the REXML.
+#
+
+require 'xmlparser'
+
+module Bio
+class Blast
+  class Report
+
+    # Specify to use XMLParser to parse XML (-m 7) output.
+    def self.xmlparser(data)
+      self.new(data, :xmlparser)
+    end
+
+    private
+
+    def xmlparser_parse(xml)
+      parser = XMLParser.new
+      def parser.default; end
+       
+      begin
+        tag_stack = Array.new
+        hash = Hash.new
+
+        parser.parse(xml) do |type, name, data|
+          case type
+          when XMLParser::START_ELEM
+            tag_stack.push(name)
+            hash.update(data)
+            case name
+            when 'Iteration'
+              iteration = Iteration.new
+              @iterations.push(iteration)
+            when 'Hit'
+              hit = Hit.new
+              hit.query_id = @query_id
+              hit.query_def = @query_def
+              hit.query_len = @query_len
+              @iterations.last.hits.push(hit)
+            when 'Hsp'
+              hsp = Hsp.new
+              @iterations.last.hits.last.hsps.push(hsp)
+            end
+          when XMLParser::END_ELEM
+            case name
+            when /^BlastOutput/
+              xmlparser_parse_program(name,hash)
+              hash = Hash.new
+            when /^Parameters$/
+              xmlparser_parse_parameters(hash)
+              hash = Hash.new
+            when /^Iteration/
+              xmlparser_parse_iteration(name, hash)
+              hash = Hash.new
+            when /^Hit/
+              xmlparser_parse_hit(name, hash)
+              hash = Hash.new
+            when /^Hsp$/
+              xmlparser_parse_hsp(hash)
+              hash = Hash.new
+            when /^Statistics$/
+              xmlparser_parse_statistics(hash)
+              hash = Hash.new
+            end
+            tag_stack.pop
+          when XMLParser::CDATA
+            if hash[tag_stack.last].nil?
+              hash[tag_stack.last] = data unless data.strip.empty?
+            else
+              hash[tag_stack.last].concat(data) if data
+            end
+          when XMLParser::PI
+          end
+        end
+      rescue XMLParserError
+        line = parser.line
+        column = parser.column
+        print "Parse error at #{line}(#{column}) : #{$!}\n"
+      end
+    end
+
+
+    def xmlparser_parse_program(tag, hash)
+      case tag
+      when 'BlastOutput_program'
+        @program = hash[tag]
+      when 'BlastOutput_version'
+        @version = hash[tag]
+      when 'BlastOutput_reference'
+        @reference = hash[tag]
+      when 'BlastOutput_db'
+        @db = hash[tag].strip
+      when 'BlastOutput_query-ID'
+        @query_id = hash[tag]
+      when 'BlastOutput_query-def'
+        @query_def = hash[tag]
+      when 'BlastOutput_query-len'
+        @query_len = hash[tag].to_i
+      end
+    end
+
+    def xmlparser_parse_parameters(hash)
+      hash.each do |k, v|
+        xml_set_parameter(k, v)
+      end
+    end
+
+    def xmlparser_parse_iteration(tag, hash)
+      case tag
+      when 'Iteration_iter-num'
+        @iterations.last.num = hash[tag].to_i
+      when 'Iteration_message'
+        @iterations.last.message = hash[tag].to_s
+
+        # for new BLAST XML format
+      when 'Iteration_query-ID'
+        @iterations.last.query_id = hash[tag].to_s
+      when 'Iteration_query-def'
+        @iterations.last.query_def = hash[tag].to_s
+      when 'Iteration_query-len'
+        @iterations.last.query_len = hash[tag].to_i
+      end
+    end
+
+    def xmlparser_parse_hit(tag, hash)
+      hit = @iterations.last.hits.last
+      case tag
+      when 'Hit_num'
+        hit.num = hash[tag].to_i
+      when 'Hit_id'
+        hit.hit_id = hash[tag].clone
+      when 'Hit_def'
+        hit.definition = hash[tag].clone
+      when 'Hit_accession'
+        hit.accession = hash[tag].clone
+      when 'Hit_len'
+        hit.len = hash[tag].clone.to_i
+      end
+    end
+
+    def xmlparser_parse_hsp(hash)
+      hsp = @iterations.last.hits.last.hsps.last
+      hsp.num          = hash['Hsp_num'].to_i
+      hsp.bit_score    = hash['Hsp_bit-score'].to_f
+      hsp.score        = hash['Hsp_score'].to_i
+      hsp.evalue       = hash['Hsp_evalue'].to_f
+      hsp.query_from   = hash['Hsp_query-from'].to_i
+      hsp.query_to     = hash['Hsp_query-to'].to_i
+      hsp.hit_from     = hash['Hsp_hit-from'].to_i
+      hsp.hit_to       = hash['Hsp_hit-to'].to_i
+      hsp.pattern_from = hash['Hsp_pattern-from'].to_i
+      hsp.pattern_to   = hash['Hsp_pattern-to'].to_i
+      hsp.query_frame  = hash['Hsp_query-frame'].to_i
+      hsp.hit_frame    = hash['Hsp_hit-frame'].to_i
+      hsp.identity     = hash['Hsp_identity'].to_i
+      hsp.positive     = hash['Hsp_positive'].to_i
+      hsp.gaps         = hash['Hsp_gaps'].to_i
+      hsp.align_len    = hash['Hsp_align-len'].to_i
+      hsp.density      = hash['Hsp_density'].to_i
+      hsp.qseq         = hash['Hsp_qseq']
+      hsp.hseq         = hash['Hsp_hseq']
+      hsp.midline      = hash['Hsp_midline']
+    end
+
+    def xmlparser_parse_statistics(hash)
+      labels = {
+        'db-num'	=> 'Statistics_db-num',
+        'db-len'	=> 'Statistics_db-len',
+        'hsp-len'	=> 'Statistics_hsp-len',
+        'eff-space'	=> 'Statistics_eff-space',
+        'kappa'	=> 'Statistics_kappa',
+        'lambda'	=> 'Statistics_lambda',
+        'entropy'	=> 'Statistics_entropy'
+      }
+      labels.each do |k,v|
+        case k
+        when 'db-num', 'db-len', 'hsp-len'
+          @iterations.last.statistics[k] = hash[v].to_i
+        else
+          @iterations.last.statistics[k] = hash[v].to_f
+        end
+      end
+    end
+        
+  end # class Report
+end # class Blast
+end # module Bio
+
+
+=begin
+
+This file is automatically loaded by bio/appl/blast/report.rb
+
+=end

metadata

@@ -0,0 +1,141 @@
+--- !ruby/object:Gem::Specification
+name: bio-blast-xmlparser
+version: !ruby/object:Gem::Version
+  version: 0.0.0
+platform: ruby
+authors:
+- BioRuby project
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2019-06-14 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bio
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 2.0.0
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 2.0.0
+- !ruby/object:Gem::Dependency
+  name: xmlparser
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.7.2
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.7.2
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '1.15'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '1.15'
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '10.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '10.0'
+- !ruby/object:Gem::Dependency
+  name: rdoc
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '5'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '5'
+- !ruby/object:Gem::Dependency
+  name: test-unit
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3'
+description: 'BioRuby BLAST XMLParser plugin: a plugin of BioRuby BLAST XML result
+  parser by using the XMLParser extension. This was formerly a part of the BioRuby
+  core ("bio" gem) and split to this gem because of the external XMLParser dependency.'
+email:
+- staff@bioruby.org
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- ".gitignore"
+- BSDL
+- COPYING
+- COPYING.ja
+- Gemfile
+- LEGAL
+- README.md
+- Rakefile
+- bio-blast-xmlparser.gemspec
+- lib/bio-blast-xmlparser.rb
+- lib/bio-blast-xmlparser/version.rb
+- lib/bio/appl/blast/xmlparser.rb
+homepage: https://github.com/bioruby/bioruby-blast-xmlparser
+licenses: []
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.7.6.2
+signing_key: 
+specification_version: 4
+summary: BioRuby BLAST XMLParser plugin
+test_files: []