bisearch_enzim_hu 0.0.3

checksums.yaml

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+SHA1:
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data/.gitignore

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+*.gem
+*.rbc
+.bundle
+.config
+.yardoc
+Gemfile.lock
+InstalledFiles
+_yardoc
+coverage
+doc/
+lib/bundler/man
+pkg
+rdoc
+spec/reports
+test/tmp
+test/version_tmp
+tmp
+*.bundle
+*.so
+*.o
+*.a
+mkmf.log

data/Gemfile

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+source 'https://rubygems.org'
+
+# Specify your gem's dependencies in bisearch_enzim_hu.gemspec
+gemspec

data/LICENSE.txt

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+Copyright (c) 2014 Iwan Buetti
+
+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.md

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+# BisearchEnzimHu
+
+A colleague of mine comes to me and expose his work problem, she would like to automatize the following steps:
+
+1. open the browser and connect to the [Primer design](http://bisearch.enzim.hu/?m=search) page of [Bisearch.enzim.hu](http://bisearch.enzim.hu/) site of Institute of Enzymology
+2. filling the form:
+  * paste a sequence like "ATTATCACA...tagtttctgcaa"
+  * check 'Bisulfite'
+  * set 'Opt' of 'Primer length' ('Primer scoring values' section) to 30
+  * set 'Minimum of CpGs' ('Primer design' section) to 0
+  * set 'Database' to 'Homo sapiens' ('Database search and fast PCR' section)
+3. Push the "Search primers" button to submit the search
+4. Wait about 30 seconds to get the 10 results
+5. For each result push the 'FPCR' (FastPCR or PCR in silico), wait about 5 seconds to get the _level2_ result
+6. Analyse the 'FPCR' result, and drop the one they have more than 1 product
+
+
+So I build this gem that automatize all the tasks in a single request (a _Wrapper_):
+
+```ruby
+require 'bisearch_enzim_hu'
+
+pd = BisearchEnzimHu::PrimerDesign.new
+pd.sequence(seq, chr, start_pos).search
+```
+
+
+
+TODO: Write a gem description
+
+## Installation
+
+Add this line to your application's Gemfile:
+
+    gem 'bisearch_enzim_hu'
+
+And then execute:
+
+    $ bundle
+
+Or install it yourself as:
+
+    $ gem install bisearch_enzim_hu
+
+## Usage
+
+```ruby
+require 'bisearch_enzim_hu'
+
+chr = "chr17"
+start_pos = 32305219
+seq = "ATTATCACACTCAGGCCCTAGCTGCTAGAAGCCTCATTTGCCTAAGTTTTTGTCCCAATGTTTCCGTGAAGGCAGAGAGAGGAGCTATTTGCATGCCAGCCCAGGGCTACGTAGAAAATATGGCAGGGATCCTCTCACACTGCAGTCGAGTCAAGGCAGTCCAGGGTGGCTGctggggccagactgccccgtcaagatccagcctgcctttcactgactgtgtgattagaatgtcttgccctatccctggactttagtttctgcaa"
+
+pd = BisearchEnzimHu::PrimerDesign.new
+pd.sequence(seq, chr, start_pos).search # chr and start_pos are optional
+File.open('result.yml', 'w') {|f| f.write pd.primers.to_yaml } # save the result (an hash) to a YAML file
+
+pd.prune # remove from result the _multi products_ FPCR results
+File.open('result_pruned.yml', 'w') {|f| f.write pd.primers.to_yaml }
+```
+
+## Contributing
+
+1. Fork it ( https://github.com/iwan/bisearch_enzim_hu/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

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+require "bundler/gem_tasks"
+

data/bisearch_enzim_hu.gemspec

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+# coding: utf-8
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'bisearch_enzim_hu/version'
+
+Gem::Specification.new do |spec|
+  spec.name          = "bisearch_enzim_hu"
+  spec.version       = BisearchEnzimHu::VERSION
+  spec.authors       = ["Iwan Buetti"]
+  spec.email         = ["iwan.buetti@gmail.com"]
+  spec.summary       = "Wrapper for Bisearch Primer Design"
+  # spec.description   = %q{TODO: Write a longer description. Optional.}
+  spec.homepage      = "https://github.com/iwan/bisearch_enzim_hu"
+  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_development_dependency "bundler", "~> 1.6"
+  spec.add_development_dependency "rake"
+  spec.add_development_dependency "rspec", "~> 2.6"
+
+  spec.add_dependency "mechanize" # http://mechanize.rubyforge.org/Mechanize.html
+  spec.add_dependency "nokogiri" # http://mechanize.rubyforge.org/Mechanize.html
+  
+end

data/lib/bisearch_enzim_hu/fpcr_submitter.rb

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+require 'net/http'
+require_relative 'l2_result_page'
+
+module BisearchEnzimHu
+
+  URL = "http://bisearch.enzim.hu/?run"
+  class FpcrSubmitter
+    def initialize(url=URL)
+      @url = url
+    end
+    
+
+    def run(hash, index)
+      fp   = hash[:fp] || hash[:line_a][:seq] # forward primer
+      rp   = hash[:rp] || hash[:line_b][:seq] # reverse primer
+      fpcr = "#{fp}!#{rp}"
+      db   = "Homo sapiens"
+
+      params = {
+        "bis" => "on", # bisulfite
+        "db" => db, # database
+        "fp" => fp, # forward primer
+        "fpcr" => fpcr, # 
+        "fpcr_but.x" => "35",
+        "fpcr_but.y" => "6",
+        "mm" => "0000000011111111", # mismatches
+        "npcrres" => "100", # PCR product to show
+        "nprimerres" => "100", # Primer matches to show
+        "prg" => "cgi/fpcr.cgi", 
+        "rp" => rp # reverse primer
+      }
+
+      uri = URI(@url)
+      puts "---> starting FPCR"
+      t = Time.now
+      page = Net::HTTP.post_form(uri, params)
+      puts "---> FPCR completed (time: #{Time.now-t}s)"
+
+      puts "--- save result to file: fpcr_result_#{index}.html"
+      File.open("fpcr_result_#{index}.html", 'w') {|f| f.write page.body }
+      
+      result_page = BisearchEnzimHu::L2ResultPage.new(page.body)
+      result_page.parse # return an hash
+    end
+    
+  end
+
+
+end

data/lib/bisearch_enzim_hu/l1_result_page.rb

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+require 'nokogiri'
+require_relative 'fpcr_submitter'
+
+module BisearchEnzimHu
+  
+  class L1ResultPage
+    def initialize(f)
+      @doc = Nokogiri::HTML(f)
+      @table_hash = nil
+    end
+    
+    def parse(deep=false)
+      # select the table after the sequence: h2,h3,input
+      table = @doc.css("h2+h3+input+table").first
+      rows  = table.css("tr")
+      header = rows.shift
+
+      @table_hash = {}
+      while !rows.empty?
+        # line_a, line_b = rows.shift(2)
+        line_a = rows.shift.css("td")
+        line_bb = rows.shift
+        line_b = line_bb.css("td")
+        hh = { :line_a => line_a, :line_b => line_b }
+        h = {}
+        # 
+        index = line_a[0].content.to_i
+        # h[:index] = index
+        h[:score] = line_a[1].content.to_f
+        h[:pa]    = line_a[11].content.to_i
+        h[:pea]   = line_a[12].content.to_i
+        h[:len]   = line_a[13].content.to_i
+
+        h[:fp]    = line_bb.css("input").select{|el| el["name"]=="fp"}.first
+        h[:fp]    = h[:fp]["value"] if !h[:fp].nil?
+
+        h[:rp]    = line_bb.css("input").select{|el| el["name"]=="rp"}.first
+        h[:rp]    = h[:rp]["value"] if !h[:rp].nil?
+
+        hh.each_pair do |i, line|
+          h[i] = {}
+          h[i][:seq]  = line[2].content
+          h[i][:pos]  = line[3].content.to_i
+          h[i][:plen] = line[4].content.to_i
+          h[i][:gc]   = line[5].content.to_f
+          h[i][:tm]   = line[6].content.to_f
+          h[i][:otm]  = line[7].content.to_f
+          h[i][:cpg]  = line[8].content
+          h[i][:sa]   = line[9].content.to_i
+          h[i][:sea]  = line[10].content.to_i
+        end
+        @table_hash[index] = h
+      end
+
+      proceed if deep
+      @table_hash
+    end
+
+    private
+
+    def proceed
+      @table_hash.each_pair do |index, hash|
+        l2_result_hash = BisearchEnzimHu::FpcrSubmitter.new.run(hash, index)
+        
+        @table_hash[index][:fpcr] = l2_result_hash
+      end
+    end
+  end
+end
+
+
+# f = File.open("first_step_page.html")
+# page = BisearchEnzimHu::L1ResultPage.new(f)
+
+# puts page.parse

data/lib/bisearch_enzim_hu/l2_result_page.rb

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+require 'nokogiri'
+require 'uri'
+
+# parsa, legge e memorizza in un hash il contenuto della pagina 
+# html con i risultati del secondo step
+
+module BisearchEnzimHu
+  
+  class L2ResultPage
+    HEAD = :head
+    SENSE = :sense
+    ANTISENSE = :antisense
+    
+
+    def initialize(f)
+      @doc = Nokogiri::HTML(f)
+      @direction = HEAD
+      @hash = nil
+    end
+    
+    def parse
+      @hash = {}
+      @doc.css("div.main").children.each_with_index do |el, i|
+
+        d = detect_direction(el)
+        if !d.nil?
+          @direction = d
+          @hash[@direction]           ||={}
+          @hash[@direction][:results] ||=[]
+          @hash[@direction][:matches]   ={}
+        end
+
+        detect_result(el)
+        detect_matches(el, i)
+      end
+      @hash
+    end
+
+    private
+
+    def detect_direction(el)
+      if el.name=="h2"
+        el.children.each do |el2|
+          if el2.name=="a" && el2["name"]=="spcr"
+            return SENSE
+          elsif el2.name=="a" && el2["name"]=="aspcr"
+            return ANTISENSE
+          end
+        end
+      end
+      nil
+    end
+
+    def detect_result(el)
+      if el.name=="pre"
+        el.children.each do |el2|
+          if el2.name=="a"
+            @hash[@direction][:results] << parse_ensembl_url(el2["href"])
+          end
+        end
+      end
+    end
+
+    def detect_matches(el, i)
+      if el.name.downcase=="h3" && el.children[0].name.downcase=="a" # && el.children[0]["name"]=~/^primer_s/
+        if el.children[0]["name"]=="primer_senfp" # Matches of forward primer
+          @hash[@direction][:matches][:forward] = @doc.css("div.main").children[i+1].content.to_i
+        elsif el.children[0]["name"]=="primer_senrp" # Matches of reverse primer
+          @hash[@direction][:matches][:reverse] = @doc.css("div.main").children[i+1].content.to_i
+        end
+      end
+    end
+
+    def parse_ensembl_url(uri)
+      h = {}
+      h[:url] = uri
+      uri = URI(uri)
+      uri.query.split("&").each do |pair|
+        k, v = pair.split("=")
+        if v
+          k = k.to_sym
+          v = v.to_i if [:start, :end].include? k
+          h[k] = v
+        end
+      end
+      h[:length] = h[:end] - h[:start]
+      h
+    end
+  end
+end
+
+# f = File.open("second_step_result_page_3res.html")
+# L2ResultPage.new(f).parse

data/lib/bisearch_enzim_hu/primer_design.rb

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+require 'mechanize'
+require_relative 'l1_result_page'
+
+module BisearchEnzimHu
+
+  # Primer Design Form (at http://bisearch.enzim.hu/?m=search)
+  class PrimerDesign
+    URL = "http://bisearch.enzim.hu/?m=search"
+    attr_reader :chr, :start_pos, :end_pos, :page, :form, :primers, :url
+
+    def initialize(options={})
+      @agent = Mechanize.new
+      @options = default_options.merge options
+      @url = @options.delete :url
+    end
+    
+    
+    def sequence(seq, chr=nil, start_pos=nil)
+      @primers = {}
+      @chr           = chr
+      @start_pos     = start_pos
+      @end_pos       = start_pos + seq.size if start_pos
+      @options[:seq] = seq
+      prepare
+      self
+    end
+
+
+    def prepare
+      # filling form
+      @page = @agent.get(@url)
+      @form = @page.form
+      @options.each_pair do |field_name, value|
+        case get_type(field_name)
+        when :select # a dropdown
+          @form.field_with(name: field_name.to_s).options.find{|e| e.text.downcase=~Regexp.new(value.downcase)}.select
+        when :checkbox
+          @form.checkbox_with(name: field_name.to_s).send(value ? :check : :uncheck)
+        when :radiobutton
+          @form.radiobutton_with(name: field_name.to_s).send(value ? :check : :uncheck)
+        when :text
+          @form.field_with(name: field_name.to_s).value=value
+        when :text_area
+          @form.field_with(name: field_name.to_s).value=value # same as text
+        end
+      end
+      self
+    end
+
+    def search(two_levels=true)
+      @primers = {}
+      puts "---> starting search primers"
+      t = Time.now
+      page = @agent.submit(@form)
+      puts "---> query completed (time: #{Time.now-t}s)"
+      @primers[:input] = {chr: @chr, start_pos: @start_pos, end_pos: @end_pos, seq: @options[:seq]}
+      res_page = BisearchEnzimHu::L1ResultPage.new(page.body)
+      # @primers[:output] = BisearchEnzimHu::L1ResultPage.new(page.body)
+      @primers[:output] = res_page.parse(two_levels)
+      self
+    end
+
+    def prune
+      indexes_to_remove = []
+      puts @primers.inspect
+      puts @primers[:output].inspect
+      @primers[:output].each_pair do |i, h|
+        puts h.inspect
+        indexes_to_remove << i if h[:fpcr][:sense][:results].size>1
+        indexes_to_remove << i if h[:fpcr][:antisense][:results].size>1
+      end
+      indexes_to_remove.uniq!
+      puts "results to remove: [#{indexes_to_remove.join(', ')}]"
+      indexes_to_remove.each{|i| @primers[:output].delete(i)}
+    end
+
+
+    private
+    def default_options
+      { 
+        bis: true,
+        optlen: 30,
+        mincpg: 0,
+        db: "homo sapiens",
+        url: URL
+      }
+    end
+
+    def get_type(field_name)
+      field_types[field_name.to_sym] || :text
+    end
+
+    def field_types
+      # default is :text
+      {
+        bis: :checkbox,
+        db: :select
+      }
+    end
+  end
+end
+
+

data/lib/bisearch_enzim_hu/version.rb

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+module BisearchEnzimHu
+  VERSION = "0.0.3"
+end

data/lib/bisearch_enzim_hu.rb

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+%w(
+    version
+    primer_design
+    l1_result_page
+    l2_result_page
+  ).each { |file| require File.join(File.dirname(__FILE__), 'bisearch_enzim_hu', file) }
+
+
+module BisearchEnzimHu
+  # Your code goes here...
+end

metadata

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+--- !ruby/object:Gem::Specification
+name: bisearch_enzim_hu
+version: !ruby/object:Gem::Version
+  version: 0.0.3
+platform: ruby
+authors:
+- Iwan Buetti
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2014-05-15 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.6'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.6'
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.6'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.6'
+- !ruby/object:Gem::Dependency
+  name: mechanize
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: nokogiri
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+description: 
+email:
+- iwan.buetti@gmail.com
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- ".gitignore"
+- Gemfile
+- LICENSE.txt
+- README.md
+- Rakefile
+- bisearch_enzim_hu.gemspec
+- lib/bisearch_enzim_hu.rb
+- lib/bisearch_enzim_hu/fpcr_submitter.rb
+- lib/bisearch_enzim_hu/l1_result_page.rb
+- lib/bisearch_enzim_hu/l2_result_page.rb
+- lib/bisearch_enzim_hu/primer_design.rb
+- lib/bisearch_enzim_hu/version.rb
+homepage: https://github.com/iwan/bisearch_enzim_hu
+licenses:
+- MIT
+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: 2.0.3
+signing_key: 
+specification_version: 4
+summary: Wrapper for Bisearch Primer Design
+test_files: []
+has_rdoc: