bisearch_enzim_hu 0.0.3
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- checksums.yaml +7 -0
- data/.gitignore +22 -0
- data/Gemfile +4 -0
- data/LICENSE.txt +22 -0
- data/README.md +68 -0
- data/Rakefile +2 -0
- data/bisearch_enzim_hu.gemspec +28 -0
- data/lib/bisearch_enzim_hu/fpcr_submitter.rb +49 -0
- data/lib/bisearch_enzim_hu/l1_result_page.rb +75 -0
- data/lib/bisearch_enzim_hu/l2_result_page.rb +93 -0
- data/lib/bisearch_enzim_hu/primer_design.rb +103 -0
- data/lib/bisearch_enzim_hu/version.rb +3 -0
- data/lib/bisearch_enzim_hu.rb +11 -0
- metadata +127 -0
checksums.yaml
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SHA1:
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metadata.gz: 138530fe7550e7d59d57f843a18d0de52c6c6f69
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SHA512:
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metadata.gz: 80922494b332ba43728a0bb9f8fbf42f53dabf676b061d8dc926ca0878536c5b8f351313374a565effcd43006398a5bc1f07ee206d549e3add9c557615398d6d
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data.tar.gz: c0323118b9ba35988b3d77071dab0db8f3187b0b3b8cc614a75b219f1f788eef7bf556b00eadaf79665315b25cf612a2f0060f05062ca5d6f82632581cf89bbf
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data/.gitignore
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*.gem
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*.rbc
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.bundle
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.config
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.yardoc
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Gemfile.lock
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InstalledFiles
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_yardoc
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coverage
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doc/
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lib/bundler/man
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pkg
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rdoc
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spec/reports
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test/tmp
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test/version_tmp
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tmp
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*.bundle
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*.so
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*.o
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*.a
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mkmf.log
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data/Gemfile
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data/LICENSE.txt
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Copyright (c) 2014 Iwan Buetti
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MIT License
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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
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NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
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LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
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OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
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WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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data/README.md
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# BisearchEnzimHu
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A colleague of mine comes to me and expose his work problem, she would like to automatize the following steps:
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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
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2. filling the form:
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* paste a sequence like "ATTATCACA...tagtttctgcaa"
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* check 'Bisulfite'
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* set 'Opt' of 'Primer length' ('Primer scoring values' section) to 30
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* set 'Minimum of CpGs' ('Primer design' section) to 0
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* set 'Database' to 'Homo sapiens' ('Database search and fast PCR' section)
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3. Push the "Search primers" button to submit the search
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4. Wait about 30 seconds to get the 10 results
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5. For each result push the 'FPCR' (FastPCR or PCR in silico), wait about 5 seconds to get the _level2_ result
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6. Analyse the 'FPCR' result, and drop the one they have more than 1 product
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So I build this gem that automatize all the tasks in a single request (a _Wrapper_):
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```ruby
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require 'bisearch_enzim_hu'
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pd = BisearchEnzimHu::PrimerDesign.new
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pd.sequence(seq, chr, start_pos).search
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```
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TODO: Write a gem description
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## Installation
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Add this line to your application's Gemfile:
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gem 'bisearch_enzim_hu'
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And then execute:
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$ bundle
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Or install it yourself as:
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$ gem install bisearch_enzim_hu
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## Usage
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```ruby
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require 'bisearch_enzim_hu'
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chr = "chr17"
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start_pos = 32305219
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seq = "ATTATCACACTCAGGCCCTAGCTGCTAGAAGCCTCATTTGCCTAAGTTTTTGTCCCAATGTTTCCGTGAAGGCAGAGAGAGGAGCTATTTGCATGCCAGCCCAGGGCTACGTAGAAAATATGGCAGGGATCCTCTCACACTGCAGTCGAGTCAAGGCAGTCCAGGGTGGCTGctggggccagactgccccgtcaagatccagcctgcctttcactgactgtgtgattagaatgtcttgccctatccctggactttagtttctgcaa"
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pd = BisearchEnzimHu::PrimerDesign.new
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pd.sequence(seq, chr, start_pos).search # chr and start_pos are optional
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File.open('result.yml', 'w') {|f| f.write pd.primers.to_yaml } # save the result (an hash) to a YAML file
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pd.prune # remove from result the _multi products_ FPCR results
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File.open('result_pruned.yml', 'w') {|f| f.write pd.primers.to_yaml }
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```
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## Contributing
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1. Fork it ( https://github.com/iwan/bisearch_enzim_hu/fork )
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2. Create your feature branch (`git checkout -b my-new-feature`)
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3. Commit your changes (`git commit -am 'Add some feature'`)
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4. Push to the branch (`git push origin my-new-feature`)
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5. Create a new Pull Request
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data/Rakefile
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# coding: utf-8
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lib = File.expand_path('../lib', __FILE__)
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$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
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require 'bisearch_enzim_hu/version'
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Gem::Specification.new do |spec|
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spec.name = "bisearch_enzim_hu"
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spec.version = BisearchEnzimHu::VERSION
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spec.authors = ["Iwan Buetti"]
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spec.email = ["iwan.buetti@gmail.com"]
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spec.summary = "Wrapper for Bisearch Primer Design"
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# spec.description = %q{TODO: Write a longer description. Optional.}
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spec.homepage = "https://github.com/iwan/bisearch_enzim_hu"
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spec.license = "MIT"
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spec.files = `git ls-files -z`.split("\x0")
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spec.executables = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
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spec.test_files = spec.files.grep(%r{^(test|spec|features)/})
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spec.require_paths = ["lib"]
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spec.add_development_dependency "bundler", "~> 1.6"
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spec.add_development_dependency "rake"
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spec.add_development_dependency "rspec", "~> 2.6"
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spec.add_dependency "mechanize" # http://mechanize.rubyforge.org/Mechanize.html
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spec.add_dependency "nokogiri" # http://mechanize.rubyforge.org/Mechanize.html
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end
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require 'net/http'
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require_relative 'l2_result_page'
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module BisearchEnzimHu
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URL = "http://bisearch.enzim.hu/?run"
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class FpcrSubmitter
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def initialize(url=URL)
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@url = url
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end
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def run(hash, index)
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fp = hash[:fp] || hash[:line_a][:seq] # forward primer
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rp = hash[:rp] || hash[:line_b][:seq] # reverse primer
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fpcr = "#{fp}!#{rp}"
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db = "Homo sapiens"
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params = {
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"bis" => "on", # bisulfite
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"db" => db, # database
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"fp" => fp, # forward primer
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"fpcr" => fpcr, #
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"fpcr_but.x" => "35",
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"fpcr_but.y" => "6",
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"mm" => "0000000011111111", # mismatches
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"npcrres" => "100", # PCR product to show
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"nprimerres" => "100", # Primer matches to show
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"prg" => "cgi/fpcr.cgi",
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"rp" => rp # reverse primer
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}
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uri = URI(@url)
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puts "---> starting FPCR"
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t = Time.now
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page = Net::HTTP.post_form(uri, params)
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puts "---> FPCR completed (time: #{Time.now-t}s)"
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puts "--- save result to file: fpcr_result_#{index}.html"
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File.open("fpcr_result_#{index}.html", 'w') {|f| f.write page.body }
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result_page = BisearchEnzimHu::L2ResultPage.new(page.body)
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result_page.parse # return an hash
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end
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end
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end
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require 'nokogiri'
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require_relative 'fpcr_submitter'
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module BisearchEnzimHu
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class L1ResultPage
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def initialize(f)
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@doc = Nokogiri::HTML(f)
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@table_hash = nil
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end
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def parse(deep=false)
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# select the table after the sequence: h2,h3,input
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table = @doc.css("h2+h3+input+table").first
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rows = table.css("tr")
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header = rows.shift
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@table_hash = {}
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while !rows.empty?
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# line_a, line_b = rows.shift(2)
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line_a = rows.shift.css("td")
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line_bb = rows.shift
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line_b = line_bb.css("td")
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hh = { :line_a => line_a, :line_b => line_b }
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h = {}
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#
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index = line_a[0].content.to_i
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# h[:index] = index
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h[:score] = line_a[1].content.to_f
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h[:pa] = line_a[11].content.to_i
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h[:pea] = line_a[12].content.to_i
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h[:len] = line_a[13].content.to_i
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h[:fp] = line_bb.css("input").select{|el| el["name"]=="fp"}.first
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h[:fp] = h[:fp]["value"] if !h[:fp].nil?
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h[:rp] = line_bb.css("input").select{|el| el["name"]=="rp"}.first
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h[:rp] = h[:rp]["value"] if !h[:rp].nil?
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hh.each_pair do |i, line|
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h[i] = {}
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h[i][:seq] = line[2].content
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h[i][:pos] = line[3].content.to_i
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h[i][:plen] = line[4].content.to_i
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h[i][:gc] = line[5].content.to_f
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h[i][:tm] = line[6].content.to_f
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h[i][:otm] = line[7].content.to_f
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h[i][:cpg] = line[8].content
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h[i][:sa] = line[9].content.to_i
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h[i][:sea] = line[10].content.to_i
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end
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@table_hash[index] = h
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end
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proceed if deep
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@table_hash
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end
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private
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def proceed
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@table_hash.each_pair do |index, hash|
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l2_result_hash = BisearchEnzimHu::FpcrSubmitter.new.run(hash, index)
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@table_hash[index][:fpcr] = l2_result_hash
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end
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end
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end
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end
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# f = File.open("first_step_page.html")
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# page = BisearchEnzimHu::L1ResultPage.new(f)
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# puts page.parse
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require 'nokogiri'
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require 'uri'
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# parsa, legge e memorizza in un hash il contenuto della pagina
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# html con i risultati del secondo step
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module BisearchEnzimHu
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class L2ResultPage
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HEAD = :head
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SENSE = :sense
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ANTISENSE = :antisense
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def initialize(f)
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@doc = Nokogiri::HTML(f)
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@direction = HEAD
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@hash = nil
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end
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def parse
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@hash = {}
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@doc.css("div.main").children.each_with_index do |el, i|
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d = detect_direction(el)
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if !d.nil?
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@direction = d
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@hash[@direction] ||={}
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@hash[@direction][:results] ||=[]
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@hash[@direction][:matches] ={}
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end
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detect_result(el)
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detect_matches(el, i)
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end
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@hash
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end
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private
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def detect_direction(el)
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if el.name=="h2"
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el.children.each do |el2|
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if el2.name=="a" && el2["name"]=="spcr"
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return SENSE
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elsif el2.name=="a" && el2["name"]=="aspcr"
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return ANTISENSE
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end
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end
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end
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nil
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end
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def detect_result(el)
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if el.name=="pre"
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el.children.each do |el2|
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if el2.name=="a"
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@hash[@direction][:results] << parse_ensembl_url(el2["href"])
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end
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end
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end
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end
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def detect_matches(el, i)
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if el.name.downcase=="h3" && el.children[0].name.downcase=="a" # && el.children[0]["name"]=~/^primer_s/
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if el.children[0]["name"]=="primer_senfp" # Matches of forward primer
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@hash[@direction][:matches][:forward] = @doc.css("div.main").children[i+1].content.to_i
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|
+
elsif el.children[0]["name"]=="primer_senrp" # Matches of reverse primer
|
69
|
+
@hash[@direction][:matches][:reverse] = @doc.css("div.main").children[i+1].content.to_i
|
70
|
+
end
|
71
|
+
end
|
72
|
+
end
|
73
|
+
|
74
|
+
def parse_ensembl_url(uri)
|
75
|
+
h = {}
|
76
|
+
h[:url] = uri
|
77
|
+
uri = URI(uri)
|
78
|
+
uri.query.split("&").each do |pair|
|
79
|
+
k, v = pair.split("=")
|
80
|
+
if v
|
81
|
+
k = k.to_sym
|
82
|
+
v = v.to_i if [:start, :end].include? k
|
83
|
+
h[k] = v
|
84
|
+
end
|
85
|
+
end
|
86
|
+
h[:length] = h[:end] - h[:start]
|
87
|
+
h
|
88
|
+
end
|
89
|
+
end
|
90
|
+
end
|
91
|
+
|
92
|
+
# f = File.open("second_step_result_page_3res.html")
|
93
|
+
# L2ResultPage.new(f).parse
|
@@ -0,0 +1,103 @@
|
|
1
|
+
require 'mechanize'
|
2
|
+
require_relative 'l1_result_page'
|
3
|
+
|
4
|
+
module BisearchEnzimHu
|
5
|
+
|
6
|
+
# Primer Design Form (at http://bisearch.enzim.hu/?m=search)
|
7
|
+
class PrimerDesign
|
8
|
+
URL = "http://bisearch.enzim.hu/?m=search"
|
9
|
+
attr_reader :chr, :start_pos, :end_pos, :page, :form, :primers, :url
|
10
|
+
|
11
|
+
def initialize(options={})
|
12
|
+
@agent = Mechanize.new
|
13
|
+
@options = default_options.merge options
|
14
|
+
@url = @options.delete :url
|
15
|
+
end
|
16
|
+
|
17
|
+
|
18
|
+
def sequence(seq, chr=nil, start_pos=nil)
|
19
|
+
@primers = {}
|
20
|
+
@chr = chr
|
21
|
+
@start_pos = start_pos
|
22
|
+
@end_pos = start_pos + seq.size if start_pos
|
23
|
+
@options[:seq] = seq
|
24
|
+
prepare
|
25
|
+
self
|
26
|
+
end
|
27
|
+
|
28
|
+
|
29
|
+
def prepare
|
30
|
+
# filling form
|
31
|
+
@page = @agent.get(@url)
|
32
|
+
@form = @page.form
|
33
|
+
@options.each_pair do |field_name, value|
|
34
|
+
case get_type(field_name)
|
35
|
+
when :select # a dropdown
|
36
|
+
@form.field_with(name: field_name.to_s).options.find{|e| e.text.downcase=~Regexp.new(value.downcase)}.select
|
37
|
+
when :checkbox
|
38
|
+
@form.checkbox_with(name: field_name.to_s).send(value ? :check : :uncheck)
|
39
|
+
when :radiobutton
|
40
|
+
@form.radiobutton_with(name: field_name.to_s).send(value ? :check : :uncheck)
|
41
|
+
when :text
|
42
|
+
@form.field_with(name: field_name.to_s).value=value
|
43
|
+
when :text_area
|
44
|
+
@form.field_with(name: field_name.to_s).value=value # same as text
|
45
|
+
end
|
46
|
+
end
|
47
|
+
self
|
48
|
+
end
|
49
|
+
|
50
|
+
def search(two_levels=true)
|
51
|
+
@primers = {}
|
52
|
+
puts "---> starting search primers"
|
53
|
+
t = Time.now
|
54
|
+
page = @agent.submit(@form)
|
55
|
+
puts "---> query completed (time: #{Time.now-t}s)"
|
56
|
+
@primers[:input] = {chr: @chr, start_pos: @start_pos, end_pos: @end_pos, seq: @options[:seq]}
|
57
|
+
res_page = BisearchEnzimHu::L1ResultPage.new(page.body)
|
58
|
+
# @primers[:output] = BisearchEnzimHu::L1ResultPage.new(page.body)
|
59
|
+
@primers[:output] = res_page.parse(two_levels)
|
60
|
+
self
|
61
|
+
end
|
62
|
+
|
63
|
+
def prune
|
64
|
+
indexes_to_remove = []
|
65
|
+
puts @primers.inspect
|
66
|
+
puts @primers[:output].inspect
|
67
|
+
@primers[:output].each_pair do |i, h|
|
68
|
+
puts h.inspect
|
69
|
+
indexes_to_remove << i if h[:fpcr][:sense][:results].size>1
|
70
|
+
indexes_to_remove << i if h[:fpcr][:antisense][:results].size>1
|
71
|
+
end
|
72
|
+
indexes_to_remove.uniq!
|
73
|
+
puts "results to remove: [#{indexes_to_remove.join(', ')}]"
|
74
|
+
indexes_to_remove.each{|i| @primers[:output].delete(i)}
|
75
|
+
end
|
76
|
+
|
77
|
+
|
78
|
+
private
|
79
|
+
def default_options
|
80
|
+
{
|
81
|
+
bis: true,
|
82
|
+
optlen: 30,
|
83
|
+
mincpg: 0,
|
84
|
+
db: "homo sapiens",
|
85
|
+
url: URL
|
86
|
+
}
|
87
|
+
end
|
88
|
+
|
89
|
+
def get_type(field_name)
|
90
|
+
field_types[field_name.to_sym] || :text
|
91
|
+
end
|
92
|
+
|
93
|
+
def field_types
|
94
|
+
# default is :text
|
95
|
+
{
|
96
|
+
bis: :checkbox,
|
97
|
+
db: :select
|
98
|
+
}
|
99
|
+
end
|
100
|
+
end
|
101
|
+
end
|
102
|
+
|
103
|
+
|
metadata
ADDED
@@ -0,0 +1,127 @@
|
|
1
|
+
--- !ruby/object:Gem::Specification
|
2
|
+
name: bisearch_enzim_hu
|
3
|
+
version: !ruby/object:Gem::Version
|
4
|
+
version: 0.0.3
|
5
|
+
platform: ruby
|
6
|
+
authors:
|
7
|
+
- Iwan Buetti
|
8
|
+
autorequire:
|
9
|
+
bindir: bin
|
10
|
+
cert_chain: []
|
11
|
+
date: 2014-05-15 00:00:00.000000000 Z
|
12
|
+
dependencies:
|
13
|
+
- !ruby/object:Gem::Dependency
|
14
|
+
name: bundler
|
15
|
+
requirement: !ruby/object:Gem::Requirement
|
16
|
+
requirements:
|
17
|
+
- - "~>"
|
18
|
+
- !ruby/object:Gem::Version
|
19
|
+
version: '1.6'
|
20
|
+
type: :development
|
21
|
+
prerelease: false
|
22
|
+
version_requirements: !ruby/object:Gem::Requirement
|
23
|
+
requirements:
|
24
|
+
- - "~>"
|
25
|
+
- !ruby/object:Gem::Version
|
26
|
+
version: '1.6'
|
27
|
+
- !ruby/object:Gem::Dependency
|
28
|
+
name: rake
|
29
|
+
requirement: !ruby/object:Gem::Requirement
|
30
|
+
requirements:
|
31
|
+
- - ">="
|
32
|
+
- !ruby/object:Gem::Version
|
33
|
+
version: '0'
|
34
|
+
type: :development
|
35
|
+
prerelease: false
|
36
|
+
version_requirements: !ruby/object:Gem::Requirement
|
37
|
+
requirements:
|
38
|
+
- - ">="
|
39
|
+
- !ruby/object:Gem::Version
|
40
|
+
version: '0'
|
41
|
+
- !ruby/object:Gem::Dependency
|
42
|
+
name: rspec
|
43
|
+
requirement: !ruby/object:Gem::Requirement
|
44
|
+
requirements:
|
45
|
+
- - "~>"
|
46
|
+
- !ruby/object:Gem::Version
|
47
|
+
version: '2.6'
|
48
|
+
type: :development
|
49
|
+
prerelease: false
|
50
|
+
version_requirements: !ruby/object:Gem::Requirement
|
51
|
+
requirements:
|
52
|
+
- - "~>"
|
53
|
+
- !ruby/object:Gem::Version
|
54
|
+
version: '2.6'
|
55
|
+
- !ruby/object:Gem::Dependency
|
56
|
+
name: mechanize
|
57
|
+
requirement: !ruby/object:Gem::Requirement
|
58
|
+
requirements:
|
59
|
+
- - ">="
|
60
|
+
- !ruby/object:Gem::Version
|
61
|
+
version: '0'
|
62
|
+
type: :runtime
|
63
|
+
prerelease: false
|
64
|
+
version_requirements: !ruby/object:Gem::Requirement
|
65
|
+
requirements:
|
66
|
+
- - ">="
|
67
|
+
- !ruby/object:Gem::Version
|
68
|
+
version: '0'
|
69
|
+
- !ruby/object:Gem::Dependency
|
70
|
+
name: nokogiri
|
71
|
+
requirement: !ruby/object:Gem::Requirement
|
72
|
+
requirements:
|
73
|
+
- - ">="
|
74
|
+
- !ruby/object:Gem::Version
|
75
|
+
version: '0'
|
76
|
+
type: :runtime
|
77
|
+
prerelease: false
|
78
|
+
version_requirements: !ruby/object:Gem::Requirement
|
79
|
+
requirements:
|
80
|
+
- - ">="
|
81
|
+
- !ruby/object:Gem::Version
|
82
|
+
version: '0'
|
83
|
+
description:
|
84
|
+
email:
|
85
|
+
- iwan.buetti@gmail.com
|
86
|
+
executables: []
|
87
|
+
extensions: []
|
88
|
+
extra_rdoc_files: []
|
89
|
+
files:
|
90
|
+
- ".gitignore"
|
91
|
+
- Gemfile
|
92
|
+
- LICENSE.txt
|
93
|
+
- README.md
|
94
|
+
- Rakefile
|
95
|
+
- bisearch_enzim_hu.gemspec
|
96
|
+
- lib/bisearch_enzim_hu.rb
|
97
|
+
- lib/bisearch_enzim_hu/fpcr_submitter.rb
|
98
|
+
- lib/bisearch_enzim_hu/l1_result_page.rb
|
99
|
+
- lib/bisearch_enzim_hu/l2_result_page.rb
|
100
|
+
- lib/bisearch_enzim_hu/primer_design.rb
|
101
|
+
- lib/bisearch_enzim_hu/version.rb
|
102
|
+
homepage: https://github.com/iwan/bisearch_enzim_hu
|
103
|
+
licenses:
|
104
|
+
- MIT
|
105
|
+
metadata: {}
|
106
|
+
post_install_message:
|
107
|
+
rdoc_options: []
|
108
|
+
require_paths:
|
109
|
+
- lib
|
110
|
+
required_ruby_version: !ruby/object:Gem::Requirement
|
111
|
+
requirements:
|
112
|
+
- - ">="
|
113
|
+
- !ruby/object:Gem::Version
|
114
|
+
version: '0'
|
115
|
+
required_rubygems_version: !ruby/object:Gem::Requirement
|
116
|
+
requirements:
|
117
|
+
- - ">="
|
118
|
+
- !ruby/object:Gem::Version
|
119
|
+
version: '0'
|
120
|
+
requirements: []
|
121
|
+
rubyforge_project:
|
122
|
+
rubygems_version: 2.0.3
|
123
|
+
signing_key:
|
124
|
+
specification_version: 4
|
125
|
+
summary: Wrapper for Bisearch Primer Design
|
126
|
+
test_files: []
|
127
|
+
has_rdoc:
|