sequenceserver-beta 0.8.7.beta1

checksums.yaml

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data/Gemfile

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+source "http://rubygems.org"
+
+gemspec

data/LICENSE.Apache.txt

@@ -0,0 +1,176 @@
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data/LICENSE.txt

@@ -0,0 +1,69 @@
+SequenceServer (http://sequenceserver.com) 
+Copyright (c) 2010-2011  Yannick Wurm, Benjamin J. Woodcroft, Anurag Priyam. 
+
+
+1.  Definitions 
+
+The software: the SequenceServer software and associated documentation. The
+term does not extend to unmodified open source software components used within
+SequenceServer which are governed by their own license agreements. However,
+modfications to such components shall be deemed a part of the SequenceServer
+software.
+
+The authors: Yannick Wurm, Anurag Priyam, Benjamin J. Woodcroft. 
+
+
+2. Fair usage
+
+Within not-for-profit and educational organizations the software can 
+be freely used by individuals and on internal and public websites.
+
+Installation of the software or use of the software by for-profit 
+organizations (including but not limited to companies, service providers 
+and consultancies) requires purchase of a usage license or other specific
+arrangements with the authors.
+
+
+3. Modifications
+
+Modifications can be made by not-for-profit and educational organizations. 
+However, citation requests and links to sequenceserver.com must remain
+visible and unaltered. 
+
+
+4. Redistribution of the software
+
+Redistribution without modification is permitted unless associated to 
+a financial transaction. In particular, the software may not be 
+distributed with nor installed via a commercial software package, nor 
+be made available by commercial service providers.  
+
+Redistribution with modification is permitted only if ALL of the 
+following conditions are respected:
+
+   a. no financial transaction is associated (see above). 
+   b. This license and copyright notices are included and remain
+      unchanged; citation requests and links to sequenceserver.com 
+      remain visible and unaltered. 
+   c. Modifications are made freely available on github.com (or an 
+      equivalent medium) and the authors are allowed to freely 
+      incorporate modifications into the software.
+
+
+5. Specific needs
+
+The authors reserve the right to make specific licensing, modification 
+and distribution  arrangements with interested parties. 
+
+
+6. Disclaimer
+
+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. 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.txt

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+Thanks for downloading SequenceServer!
+
+Documentation available at http://www.sequenceserver.com
+
+-- Yannick Wurm, Ben Woodcroft, Anurag Priyam

data/bin/sequenceserver

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+#!/usr/bin/env ruby
+
+require 'rubygems'
+require 'bundler/setup'
+require 'optparse'
+require 'sequenceserver'
+
+# e.g:
+# sequenceserver --config .sequenceserver.conf format_database
+begin
+  # parse command line till first non-option, removing parsed options from ARGV
+  OptionParser.new do |opts|
+    opts.banner =<<BANNER
+
+SUMMARY
+
+  custom, local, BLAST server
+
+USAGE
+
+  sequenceserver [options] [subcommand] [subcommand's options]
+
+  Example:
+
+    # launch SequenceServer with the given config file
+    $ sequenceserver --config ~/.sequenceserver.ants.conf
+
+    # use the bundled database formatter utility to prepare databases for use
+    # with SequenceServer
+    $ sequenceserver format-databases
+
+DESCRIPTION
+
+  SequenceServer lets you rapidly set up a BLAST+ server with an intuitive user
+  interface for use locally or over the web.
+
+SUB-COMMANDS
+
+  format-databases:
+    prepare BLAST databases for use with SequenceServer
+
+    Run '#{$0} format-databases -h' for help.
+
+OPTIONS
+
+BANNER
+    opts.on('-c', '--config CONFIG_FILE', 'Use the given configuration file') do |config_file|
+      SequenceServer::App.config_file = File.expand_path(config_file)
+    end
+
+    opts.on('-v', '--version', 'Print version number of SequenceServer that will be loaded.' ) do |config_file|
+      puts SequenceServer.version
+      exit
+    end
+  end.order!
+
+  # of the remaining items in ARGV, the first one must be a subcommand
+  subcommand = ARGV.shift
+
+  if subcommand
+    # process subcommands now
+
+    case subcommand
+    when 'format-databases'
+      require 'sequenceserver/database_formatter'
+      exit
+    else
+      puts "invalid subcommand: #{subcommand}"
+      puts "Run '#{$0} -h' for help with command line options."
+      exit
+    end
+  end
+rescue OptionParser::InvalidOption =>e
+  puts e
+  puts "Run '#{$0} -h' for help with command line options."
+  exit
+end
+
+# display name for tools like `ps`
+$PROGRAM_NAME = 'sequenceserver'
+
+SequenceServer::App.run!

data/config.ru

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+require 'rubygems'
+require 'bundler/setup'
+require 'sequenceserver'
+
+SequenceServer::App.init
+run SequenceServer::App

data/example.config.yml

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+# Path to the blast executables.
+# 
+# Sequence Server scans the given directory for blast binaries. Ideally it
+# should point the `bin` of your BLAST+ installation. Not setting this
+# value, or setting it to `nil` will default to searching the system `PATH`.
+#
+# Uncomment the following line, and change to appropriate value to use.
+#
+# bin: ~/ncbi-blast-2.2.25+/bin/
+
+# Path to blast database.
+#
+# Sequence Server scans the given directory (including the sub-directories)
+# for blast database. You can not specify more than one top-level directory.
+# Not setting this value, will default to searching `database` directory
+# relative to the current working directory.
+#
+# Uncomment the following line, and change to appropriate value to use.
+#
+# database: ~/blast_databases/
+
+# Port to run Sequence Server on.
+#
+# The app will then be accessible at http://your-ip:port. Defaults to 4567.
+# http://localhost:port is also valid for local access.
+#
+# Uncomment the following line, and change to appropriate value to use.
+#
+# port: 4567
+
+# number of threads to be use when blasting
+#
+# This option is passed directly to BLAST+. Setting this option to more
+# than 1 may crash BLAST+ if it was not compiled with threading support.
+# Default is to use the safe value of 1.
+#
+# Uncomment the following line, and change to appropriate value to use.
+#
+# num_threads: 1

data/lib/profile_code.rb

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+require 'ruby-prof'
+
+$:.unshift '.'
+
+#require 'sinatra/base'
+require 'yaml'
+require 'logger'
+require 'fileutils'
+require 'sequenceserver/helpers'
+require 'sequenceserver/blast'
+require 'sequenceserver/sequencehelpers'
+require 'sequenceserver/sinatralikeloggerformatter'
+require 'sequenceserver/customisation'
+require 'sequenceserver/version'
+
+require 'sequenceserver'
+
+
+query = '>1111883
+GCTGGCGGCGTGCCTAACACATGTAAGTCGAACGGGACTGGGGGCAACTCCAGTTCAGTG
+GCAGACGGGTGCGTAACACGTGAGCAACTTGTCCGACGGCGGGGGATAGCCGGCCCAACG
+GCCGGGTAATACCGCGTACGCTCGTTTAGGGACATCCCTGAATGAGGAAAGCCGTAAGGC
+ACCGACGGAGAGGCTCGCGGCCTATCAGCTAGTTGGCGGGGTAACGGCCCACCAAGGCGA
+CGACGGGTAGCTGGTCTGAGAGGATGGCCAGCCACATTGGGACTGAGACACGGCCCAGAC
+TCCTACGGGAGGCAGCAGTGGGGAATCTTGCGCAATGGCCGCAAGGCTGACGCAGCGACG
+CCGCGTGTGGGATGACGGCCTTCGGGTTGTAAACCACTGTCGGGAGGAACGAATACTCGG
+CTAGTCCGAGGGTGACGGTACCTCCAAAGGAAGCACCGGCTAACTCCGTGCCAGCAGCCG
+CGGTAATACGGAGGGTGCGAGCGTTGTCCGGAATCACTGGGCGTAAAGGGCGCGTAGGTG
+GCCCGTTAAGTGGCTGGTGAAATCCCGGGGCTCAACTCCGGGGCTGCCGGTCAGACTGGC
+GAGCTAGAGCACGGTAGGGGCAGATGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATAT
+CGGGAAGAATACCAGTGGCGAAGGCGTTCTGCTGGGCCGTTGCTGACACTGAGGCGCGAC
+AGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGGACACT
+AGACGTCGGGGGGAGCGACCCTCCCGGTGTCGTCGCTAACGCAGTAAGTGTCCCGCCTGG
+GGAGTACGGCCGCAAGGCTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGA
+GCATGTGGTTTAATTCGAAGCAACGCGAAGAACCTTACCTGGGCTTGACATGCTGGTGCA
+AGCCGGTGGAAACATCGGCCCCTCTTCGGAGCGCCAGCACAGGTGCTGCATGGCTGTCGT
+CAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACTCTCGCTCCCAGT
+TGCCAGCGGTTCGGCCGGGGACTCTGGGGGGACTGCCGGCGTTAAGCCGGAGGAAGGTGG
+GGACGACGTCAAGTCATCATGGCCCTTACGTCCAGGGCGACACACGTGCTACAATGCCTG
+GTACAGCGCGTCGCGAACTCGCAAGAGGGAGCCAATCGCCAAAAGCCGGGCTAAGTTCGG
+ATTGTCGTCTGCAACTCGACGGCATGAAGCCGGAATCGCTAGTAATCGCGGATCAGCCAC
+GCCGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACGCCATGGAAGCCGGA
+GGGACCCGAAACCGGTGGGCCAACCGCAAGGGGGCAGCCGTCTAAGGT'
+
+#blastn -db '/home/ben/git/sequenceserver/db/97_otus.fasta' -query '/tmp/sequenceserver_query20140119-10926-qt2ecp'  -task blastn  -num_threads 1 -html
+method        = 'blastn'#params['method']
+databases     = ['/home/ben/git/sequenceserver/db/97_otus.fasta']#params[:databases]
+sequence      = query #params[:sequence]
+advanced_opts = '-max_target_seqs 1'#params['advanced']
+
+# evaluate empty sequence as nil, otherwise as fasta
+#      sequence = sequence.empty? ? nil : to_fasta(sequence)
+
+# blastn implies blastn, not megablast; but let's not interfere if a user
+# specifies `task` herself
+if method == 'blastn' and not advanced_opts =~ /task/
+  #advanced_opts << ' -task blastn '
+end
+
+
+# run blast and log
+blast = SequenceServer::Blast.new(method, sequence, databases.join(' '), advanced_opts)
+blast.run!
+puts('Ran: ' + blast.command)
+
+
+    def format_blast_results(result, databases)
+      formatted_result = ''
+      @all_retrievable_ids = []
+      string_of_used_databases = databases.join(' ')
+      blast_database_number = 0
+      line_number = 0
+      started_query = false
+      finished_database_summary = false
+      finished_alignments = false
+      reference_string = ''
+      database_summary_string = ''
+      result.each do |line|
+        line_number += 1
+        next if line_number <= 5 #skip the first 5 lines
+
+        # Add the reference to the end, not the start, of the blast result
+        if line_number >= 7 and line_number <= 15
+          reference_string += line
+          next
+        end
+
+        if !finished_database_summary and line_number > 15
+          database_summary_string += line
+          finished_database_summary = true if line.match(/total letters/)
+          next
+        end
+
+        # Remove certain lines from the output
+        skipped_lines = [/^<\/BODY>/,/^<\/HTML>/,/^<\/PRE>/]
+        skip = false
+        skipped_lines.each do |skippy|
+        #  $stderr.puts "`#{line}' matches #{skippy}?"
+          if skippy.match(line)
+            skip = true
+         #   $stderr.puts 'yes'
+          else
+          #  $stderr.puts 'no'
+          end
+        end
+        next if skip
+
+        # Remove the javascript inclusion
+        line.gsub!(/^<script src=\"blastResult.js\"><\/script>/, '')
+
+        if line.match(/^>/) # If line to possibly replace
+          # Reposition the anchor to the end of the line, so that it both still works and
+          # doesn't interfere with the diagnostic space at the beginning of the line.
+          #
+          # There are two cases:
+          #
+          # database formatted _with_ -parse_seqids
+          line.gsub!(/^>(.+)(<a.*><\/a>)(.*)/, '>\1\3\2')
+          #
+          # database formatted _without_ -parse_seqids
+          line.gsub!(/^>(<a.*><\/a>)(.*)/, '>\2\1')
+
+          # get hit coordinates -- useful for linking to genome browsers
+          hit_length      = result[line_number..-1].index{|l| l =~ />lcl|Lambda/}
+          hit_coordinates = result[line_number, hit_length].grep(/Sbjct/).
+            map(&:split).map{|l| [l[1], l[-1]]}.flatten.map(&:to_i).minmax
+
+          # Create the hyperlink (if required)
+          formatted_result += construct_sequence_hyperlink_line(line, databases, hit_coordinates)
+        else
+          # Surround each query's result in <div> tags so they can be coloured by CSS
+          if matches = line.match(/^<b>Query=<\/b> (.*)/) # If starting a new query, then surround in new <div> tag, and finish the last one off
+            line = "<div class=\"resultn\" id=\"#{matches[1]}\">\n<h3>Query= #{matches[1]}</h3><pre>"
+            unless blast_database_number == 0
+              line = "</pre></div>\n#{line}"
+            end
+            blast_database_number += 1
+          elsif line.match(/^  Database: /) and !finished_alignments
+            formatted_result += "</div>\n<pre>#{database_summary_string}\n\n"
+            finished_alignments = true
+          end
+          formatted_result += line
+        end
+      end
+      formatted_result << "</pre>"
+
+      link_to_fasta_of_all = "/get_sequence/?id=#{@all_retrievable_ids.join(' ')}&db=#{string_of_used_databases}"
+      # #dbs must be sep by ' '
+      retrieval_text       = @all_retrievable_ids.empty? ? '' : "<a href='#{url(link_to_fasta_of_all)}'>FASTA of #{@all_retrievable_ids.length} retrievable hit(s)</a>"
+
+      "<h2>Results</h2>"+
+      retrieval_text +
+      "<br/><br/>" +
+      formatted_result +
+      "<br/>" +
+      "<pre>#{reference_string.strip}</pre>"
+    end
+
+    def construct_sequence_hyperlink_line(line, databases, hit_coordinates)
+      matches = line.match(/^>(.+)/)
+      sequence_id = matches[1]
+
+      link = nil
+
+      # If a custom sequence hyperlink method has been defined,
+      # use that.
+      options = {
+        :sequence_id => sequence_id,
+        :databases => databases,
+        :hit_coordinates => hit_coordinates
+      }
+
+      # First precedence: construct the whole line to be customised
+      if self.respond_to?(:construct_custom_sequence_hyperlinking_line)
+        settings.log.debug("Using custom hyperlinking line creator with sequence #{options.inspect}")
+        link_line = construct_custom_sequence_hyperlinking_line(options)
+        unless link_line.nil?
+          return link_line
+        end
+      end
+
+      # If we have reached here, custom construction of the
+      # whole line either wasn't defined, or returned nil
+      # (indicating failure)
+      if self.respond_to?(:construct_custom_sequence_hyperlink)
+ #       settings.log.debug("Using custom hyperlink creator with sequence #{options.inspect}")
+        link = construct_custom_sequence_hyperlink(options)
+      else
+#        settings.log.debug("Using standard hyperlink creator with sequence `#{options.inspect}'")
+        link = construct_standard_sequence_hyperlink(options)
+      end
+
+      # Return the BLAST output line with the link in it
+      if link.nil?
+  #      settings.log.debug('No link added link for: `'+ sequence_id +'\'')
+        return line
+      else
+        settings.log.debug('Added link for: `'+ sequence_id +'\''+ link)
+        return "><a href='#{url(link)}' target='_blank'>#{sequence_id}</a> \n"
+      end
+
+    end
+
+    # Advanced options are specified by the user. Here they are checked for interference with SequenceServer operations.
+    # raise ArgumentError if an error has occurred, otherwise return without value
+    def validate_advanced_parameters(advanced_options)
+      raise ArgumentError, "Invalid characters detected in the advanced options" unless advanced_options =~ /\A[a-z0-9\-_\. ']*\Z/i
+      disallowed_options = %w(-out -html -outfmt -db -query)
+      disallowed_options.each do |o|
+        raise ArgumentError, "The advanced BLAST option \"#{o}\" is used internally by SequenceServer and so cannot be specified by the you" if advanced_options =~ /#{o}/i
+      end
+    end
+
+puts format_blast_results(blast.result, databases)
+
+
+