scbi_blast 0.0.30
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.
- data/History.txt +4 -0
- data/Manifest.txt +21 -0
- data/PostInstall.txt +7 -0
- data/README.rdoc +48 -0
- data/Rakefile +26 -0
- data/lib/scbi_blast.rb +15 -0
- data/lib/scbi_blast/batch_blast.rb +115 -0
- data/lib/scbi_blast/blast_hit.rb +115 -0
- data/lib/scbi_blast/blast_query.rb +37 -0
- data/lib/scbi_blast/blast_simplexml_result.rb +158 -0
- data/lib/scbi_blast/blast_table_result.rb +190 -0
- data/lib/scbi_blast/blast_xml_result.rb +152 -0
- data/lib/scbi_blast/dust_masker.rb +103 -0
- data/script/console +10 -0
- data/script/destroy +14 -0
- data/script/generate +14 -0
- data/test/blast.txt +252 -0
- data/test/blast.xml +173 -0
- data/test/empty_blast.xml +42 -0
- data/test/test_helper.rb +4 -0
- data/test/test_scbi_blast.rb +178 -0
- metadata +89 -0
data/History.txt
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data/Manifest.txt
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History.txt
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Manifest.txt
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PostInstall.txt
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README.rdoc
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Rakefile
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lib/scbi_blast.rb
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script/console
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script/destroy
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script/generate
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test/test_helper.rb
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test/test_scbi_blast.rb
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test/blast.xml
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test/empty_blast.xml
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test/blast.txt
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lib/scbi_blast/blast_hit.rb
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lib/scbi_blast/blast_query.rb
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lib/scbi_blast/blast_table_result.rb
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lib/scbi_blast/blast_xml_result.rb
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lib/scbi_blast/blast_simplexml_result.rb
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lib/scbi_blast/batch_blast.rb
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lib/scbi_blast/dust_masker.rb
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data/PostInstall.txt
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data/README.rdoc
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= scbi_blast
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* http://github.com/#{github_username}/#{project_name}
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== DESCRIPTION:
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FIX (describe your package)
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== FEATURES/PROBLEMS:
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* FIX (list of features or problems)
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== SYNOPSIS:
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FIX (code sample of usage)
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== REQUIREMENTS:
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* FIX (list of requirements)
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== INSTALL:
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* FIX (sudo gem install, anything else)
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== LICENSE:
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(The MIT License)
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Copyright (c) 2010 Dario Guerrero
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Permission is hereby granted, free of charge, to any person obtaining
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a copy of this software and associated documentation files (the
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'Software'), to deal in the Software without restriction, including
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without limitation the rights to use, copy, modify, merge, publish,
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distribute, sublicense, and/or sell copies of the Software, and to
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permit persons to whom the Software is furnished to do so, subject to
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the following conditions:
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The above copyright notice and this permission notice shall be
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included in all copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED 'AS IS', WITHOUT WARRANTY OF ANY KIND,
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EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
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MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
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IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
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CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
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TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
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SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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data/Rakefile
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require 'rubygems'
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gem 'hoe', '>= 2.1.0'
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require 'hoe'
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require 'fileutils'
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require './lib/scbi_blast'
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Hoe.plugin :newgem
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# Hoe.plugin :website
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# Hoe.plugin :cucumberfeatures
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# Generate all the Rake tasks
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# Run 'rake -T' to see list of generated tasks (from gem root directory)
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$hoe = Hoe.spec 'scbi_blast' do
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self.developer 'Dario Guerrero & Almudena Bocinos', 'dariogf@gmail.com, alkoke@gmail.com'
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self.post_install_message = 'PostInstall.txt' # TODO remove if post-install message not required
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self.rubyforge_name = self.name # TODO this is default value
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# self.extra_deps = [['activesupport','>= 2.0.2']]
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end
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require 'newgem/tasks'
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Dir['tasks/**/*.rake'].each { |t| load t }
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# TODO - want other tests/tasks run by default? Add them to the list
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# remove_task :default
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# task :default => [:spec, :features]
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data/lib/scbi_blast.rb
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$: << File.join(File.dirname(__FILE__),File.basename(__FILE__,File.extname(__FILE__)))
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require 'batch_blast'
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require 'dust_masker'
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require 'blast_query'
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# require 'blast_xml_result'
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require 'blast_simplexml_result'
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require 'blast_hit'
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require 'blast_table_result'
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module ScbiBlast
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VERSION = '0.0.30'
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end
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#!/usr/bin/env ruby
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class BatchBlast
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def initialize(database, blast_type = 'blastn', extra_params = '')
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@blast_type = blast_type
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@database = database
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@extra_params = extra_params
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end
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def get_blast_cmd(fmt = :table)
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if fmt==:table
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format = ' -outfmt "7 qseqid sacc pident length mismatch gapopen qstart qend sstart send evalue bitscore score qframe sframe qseq sseq" '
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elsif fmt ==:xml
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format = ' -outfmt 5 '
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end
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dust=''
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#disable dust flag if blastn
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# if @blast_type.index('blastn')
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# dust=' -dust no '
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# end
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cmd = @blast_type+' '+dust+@extra_params + format + @database
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return cmd
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end
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def do_blast(seqs, fmt = :table,parse_output=true)
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if seqs.is_a?(Array)
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seq_fasta=seqs.join("\n")
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else
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seq_fasta=seqs
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end
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cmd = get_blast_cmd(fmt)
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res=''
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# Ojo, que una vez nos ibamos a volver locos buscando porque esto no devolvia todos los hits que se encontraban al ejecutar el blast a mano, y era porque en el blast a mano le estabamos pasando la secuencia completa mientras que en el MID le estabamos pasando sólo los 20 primeros nt.
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IO.popen(cmd,'w+') {|blast|
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blast.sync = true
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blast.write(seq_fasta)
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blast.close_write
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res = blast.readlines
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blast.close_read
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}
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if !$?.exitstatus.nil? && $?.exitstatus>0
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raise "Error doing blast #{cmd} to fasta: #{seq_fasta}"
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end
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# check if all sequences where processed
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if parse_output
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if fmt == :table
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res = BlastTableResult.new(res)
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elsif fmt == :xml
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res = BlastSimplexmlResult.new(res)
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# elsif fmt ==:xml2
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# res = BlastXmlResult.new(res)
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end
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# puts "#{seq_fasta.count('>')}, #{res.querys.count}"
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if seq_fasta.count('>')!=res.querys.count
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not_processed = seqs.select{|e| e.index('>')}
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res.querys.each do |query|
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if not_processed.include?('>'+query.query_id)
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not_processed.delete('>'+query.query_id)
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end
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end
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raise "These sequences #{seq_fasta.count('>')},#{res.querys.count} where not processed by #{cmd}:\n #{not_processed} \n Full_data:\n seqs=#{seqs};\n"
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end
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end
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return res
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end
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def do_blast_seqs(seqs, fmt = :table,parse_output=true)
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cmd = get_blast_cmd(fmt)
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fastas=[]
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seqs.each do |seq|
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fastas.push '>'+seq.seq_name
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fastas.push seq.seq_fasta
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end
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return do_blast(fastas,fmt,parse_output)
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end
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def close
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end
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end
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class BlastHit
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def initialize(q_beg,q_end,s_beg,s_end)
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@q_beg = q_beg.to_i-1 #to storage in array [0 .. ]
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@q_end = q_end.to_i-1 #to storage in array [0 .. ]
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@s_beg = s_beg.to_i-1
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@s_end = s_end.to_i-1
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@reversed = false
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# TODO -Reversed should be taken from q_frame and s_frame instead of s_end. In proteins comes from q_frame. In nt from s_frames.
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if @s_beg > @s_end
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@s_beg = s_end.to_i-1
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@s_end = s_beg.to_i-1
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@reversed = true
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end
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# 2. S_ID - Subject ID.
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# 3. IDENT - Identity (%).
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# 4. ALIGN_LEN - Alignment length.
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# 5. MISMATCHES - Number of mismatches.
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# 6. GAPS - Number of gaps.
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# 7. Q_BEG - Query begin.
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# 8. Q_END - Query end.
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# 9. S_BEG - Subject begin.
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# 10. S_END - Subject end.
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# 11. E_VAL - Expect value.
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# 12. BIT_SCORE - Bit score.
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end
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def subject_id=(v)
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@subject_id = v
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end
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def ident=(v)
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@ident = v.to_f
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end
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def align_len=(v)
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@align_len = v.to_i
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end
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def mismatches=(v)
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@mismatches = v.to_i
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end
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def gaps=(v)
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@gaps = v.to_i
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end
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def e_val=(v)
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@e_val = v.to_f
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end
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def bit_score=(v)
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@bit_score = v.to_f
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end
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def score=(v)
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@score = v.to_f
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end
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def acc=(v)
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@acc = v
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end
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def definition=(v)
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@definition = v
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end
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def q_frame=(v)
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@q_frame = v.to_i
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end
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def s_frame=(v)
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@s_frame = v.to_i
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end
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def s_seq=(v)
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@s_seq = v
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end
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def q_seq=(v)
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@q_seq = v
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end
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def full_subject_length=(v)
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@full_subject_length = v
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end
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def inspect
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res = "Hit: #{@subject_id.ljust(10)} #{@ident.to_s.rjust(4)} #{@align_len.to_s.rjust(2)} #{@mismatches.to_s.rjust(2)} #{@gaps.to_s.rjust(2)} #{@q_beg.to_s.rjust(5)} #{@q_end.to_s.rjust(5)} #{@s_beg.to_s.rjust(5)} #{@s_end.to_s.rjust(5)} #{@e_val.to_s.rjust(5)} #{@bit_score.to_s.rjust(5)} #{@reversed.to_s.rjust(5)}"
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res += " #{@score.to_s.rjust(5)} #{@acc.ljust(10)} #{@definition.ljust(10)} #{@q_frame.to_s.rjust(2)} #{@s_frame.to_s.rjust(2)} #{@full_subject_length.to_s.rjust(5)} #{@q_seq}.#{@s_seq}."
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return res
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end
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def get_subject
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return @subject_id
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end
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attr_accessor :q_beg, :q_end, :s_beg, :s_end
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attr_reader :subject_id, :align_len, :gaps, :mismatches
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attr_accessor :reversed
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attr_reader :score, :acc, :definition, :q_frame, :s_frame, :full_subject_length, :ident, :e_val, :bit_score
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attr_reader :q_seq, :s_seq
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end
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class BlastQuery
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attr_accessor :hits
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attr_accessor :query_id, :query_def, :full_query_length
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def initialize(query_id)
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@query_id = query_id
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@query_def = query_id
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@full_query_length = 0
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@hits = []
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# inspect
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end
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def add_hit(h)
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@hits.push h
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end
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def inspect
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res = "\n * Query #{@query_id} :"
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res += "subject_id ident align_len mismatches gaps q_beg q_end s_beg s_end e_val bit_score reversed\n\n"
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@hits.each{ |h| res+= h.inspect+"\n" }
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return res
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end
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def size
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return @hits.size
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+
end
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+
|
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def sort(comand)
|
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return @hits.sort(comand)
|
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+
end
|
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+
|
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|
+
end
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+
|
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+
|
@@ -0,0 +1,158 @@
|
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1
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+
require "blast_query.rb"
|
2
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+
require "blast_hit.rb"
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3
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+
|
4
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+
require 'zlib'
|
5
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+
require 'xmlsimple'
|
6
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+
#xml=File.open('orf.1.xml').read
|
7
|
+
#data = XmlSimple.xml_in(xml)
|
8
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+
#
|
9
|
+
#
|
10
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+
#data['best_orf'][0]['start'][0]
|
11
|
+
#data['best_orf'][0]['content']
|
12
|
+
|
13
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+
######################################
|
14
|
+
# Author:: Almudena Bocinos Rioboo
|
15
|
+
# Extracts results from blast table's file and uses it to create instances of "BlastQuery" and "BlastHit"
|
16
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+
|
17
|
+
######################################
|
18
|
+
|
19
|
+
class BlastSimplexmlResult
|
20
|
+
|
21
|
+
def initialize(input)
|
22
|
+
|
23
|
+
@querys = []
|
24
|
+
lines=[]
|
25
|
+
if input.is_a?(Array)
|
26
|
+
lines=input
|
27
|
+
elsif !input.strip.empty?
|
28
|
+
if File.exists?(input)
|
29
|
+
fich = File.open(input,'r')
|
30
|
+
lines = fich.readlines
|
31
|
+
fich.close
|
32
|
+
else
|
33
|
+
raise "File #{input} doesn't exists"
|
34
|
+
end
|
35
|
+
|
36
|
+
end
|
37
|
+
|
38
|
+
# puts "lines length #{lines.length}"
|
39
|
+
if !lines.empty?
|
40
|
+
data = XmlSimple.xml_in(lines.join)
|
41
|
+
iterations = data['BlastOutput_iterations']
|
42
|
+
#require 'json'
|
43
|
+
#puts iterations.to_json
|
44
|
+
|
45
|
+
iterations[0]['Iteration'].each do |iteration|
|
46
|
+
|
47
|
+
# puts JSON::pretty_generate(iteration)
|
48
|
+
|
49
|
+
query_id = iteration['Iteration_query-ID'][0]
|
50
|
+
full_query_length = iteration['Iteration_query-len'][0]
|
51
|
+
query_def = iteration['Iteration_query-def'][0]
|
52
|
+
|
53
|
+
if query_def =~ /^([^\s]+)/
|
54
|
+
query_def=$1
|
55
|
+
end
|
56
|
+
|
57
|
+
#@query_def = iteration['Iteration_query-def'][0]
|
58
|
+
|
59
|
+
query = BlastQuery.new(query_id)
|
60
|
+
query.query_def = query_def
|
61
|
+
query.full_query_length = full_query_length
|
62
|
+
@querys.push query
|
63
|
+
|
64
|
+
|
65
|
+
|
66
|
+
hits = iteration['Iteration_hits'][0]['Hit']
|
67
|
+
if !hits.nil?
|
68
|
+
hits.each do |h|
|
69
|
+
#puts JSON::pretty_generate(h)
|
70
|
+
|
71
|
+
|
72
|
+
|
73
|
+
subject_id=h['Hit_id'][0]
|
74
|
+
acc =h['Hit_accession'][0]
|
75
|
+
full_subject_length = h['Hit_len'][0].to_i
|
76
|
+
hit_def=h['Hit_def'][0]
|
77
|
+
if hit_def=='No definition line'
|
78
|
+
hit_def =subject_id
|
79
|
+
end
|
80
|
+
|
81
|
+
hsps = h['Hit_hsps'][0]['Hsp']
|
82
|
+
|
83
|
+
hsps.each do |hsp|
|
84
|
+
|
85
|
+
q_beg=hsp['Hsp_query-from'][0].to_i
|
86
|
+
q_end=hsp['Hsp_query-to'][0].to_i
|
87
|
+
s_beg=hsp['Hsp_hit-from'][0].to_i
|
88
|
+
s_end=hsp['Hsp_hit-to'][0].to_i
|
89
|
+
|
90
|
+
# creates the hit
|
91
|
+
hit = BlastHit.new(q_beg,q_end,s_beg,s_end)
|
92
|
+
|
93
|
+
hit.align_len=hsp['Hsp_align-len'][0].to_i
|
94
|
+
hit.ident=(hsp['Hsp_identity'][0].to_f/hit.align_len)*100
|
95
|
+
hit.gaps=hsp['Hsp_gaps'][0].to_i
|
96
|
+
hit.mismatches=hsp['Hsp_midline'][0].count(' ').to_i - hit.gaps
|
97
|
+
hit.e_val=hsp['Hsp_evalue'][0].to_f
|
98
|
+
hit.e_val = (hit.e_val*1000).round/1000.0
|
99
|
+
hit.bit_score=hsp['Hsp_bit-score'][0].to_f
|
100
|
+
hit.bit_score = (hit.bit_score*100).round/100.0
|
101
|
+
|
102
|
+
hit.score = hsp['Hsp_score'][0].to_f
|
103
|
+
hit.q_frame = hsp['Hsp_query-frame'][0].to_i
|
104
|
+
hit.s_frame =hsp['Hsp_hit-frame'][0].to_i
|
105
|
+
|
106
|
+
hit.q_seq = hsp['Hsp_qseq'][0]
|
107
|
+
hit.s_seq = hsp['Hsp_hseq'][0]
|
108
|
+
|
109
|
+
|
110
|
+
hit.subject_id= subject_id
|
111
|
+
hit.full_subject_length=full_subject_length
|
112
|
+
# hit.full_query_length = full_query_length
|
113
|
+
hit.definition=hit_def
|
114
|
+
hit.acc=acc
|
115
|
+
|
116
|
+
query.add_hit(hit)
|
117
|
+
|
118
|
+
end
|
119
|
+
end
|
120
|
+
end
|
121
|
+
end
|
122
|
+
end
|
123
|
+
#inspect
|
124
|
+
end
|
125
|
+
|
126
|
+
|
127
|
+
|
128
|
+
def inspect
|
129
|
+
|
130
|
+
res = "Blast results:\n"
|
131
|
+
res+= '-'*20
|
132
|
+
res+= "\nQuerys: #{@querys.count}\n"
|
133
|
+
@querys.each{|q| res+=q.inspect+"\n"}
|
134
|
+
return res
|
135
|
+
end
|
136
|
+
|
137
|
+
def find_query(querys,name_q)
|
138
|
+
# newq = querys.find{|q| ( q.find{|h| (h.subject_id)})}
|
139
|
+
new_q=nil
|
140
|
+
|
141
|
+
if !querys.empty?
|
142
|
+
new_q=querys.find{|q| (q.query_id==name_q)}
|
143
|
+
end
|
144
|
+
|
145
|
+
return new_q
|
146
|
+
end
|
147
|
+
|
148
|
+
def empty?
|
149
|
+
|
150
|
+
return @querys.empty?
|
151
|
+
end
|
152
|
+
|
153
|
+
def size
|
154
|
+
@querys.size
|
155
|
+
end
|
156
|
+
|
157
|
+
attr_accessor :querys
|
158
|
+
end
|