bel 0.2.1 → 0.3.0.beta1
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- data/INSTALL.md +19 -0
- data/INSTALL_RUBY.md +107 -0
- data/README.md +319 -0
- data/bel.gemspec +67 -0
- data/bin/bel2rdf +134 -0
- data/bin/bel_compare +177 -0
- data/bin/bel_parse +60 -0
- data/bin/bel_rdfschema +72 -0
- data/bin/bel_summarize +86 -0
- data/bin/bel_upgrade +77 -55
- data/bin/bel_upgrade_term +163 -0
- data/ext/mri/bel-ast.c +221 -0
- data/ext/mri/bel-ast.h +82 -0
- data/ext/mri/bel-node-stack.c +83 -0
- data/ext/mri/bel-node-stack.h +26 -0
- data/ext/mri/bel-parse-statement.c +122296 -0
- data/ext/mri/bel-parse-term.c +117670 -0
- data/ext/mri/bel-parser.c +91 -0
- data/ext/mri/bel-parser.h +13 -0
- data/ext/mri/bel-token.c +161 -0
- data/ext/mri/bel-token.h +58 -0
- data/ext/mri/bel-tokenize-term.c +391 -0
- data/ext/mri/extconf.rb +8 -0
- data/ext/mri/libbel.c +5 -0
- data/ext/mri/libbel.def +26 -0
- data/lib/bel.rb +12 -2
- data/lib/bel/completion.rb +53 -0
- data/lib/bel/completion_rule.rb +236 -0
- data/lib/bel/language.rb +573 -97
- data/lib/bel/namespace.rb +237 -21
- data/lib/bel/quoting.rb +29 -0
- data/lib/bel/rdf.rb +314 -0
- data/lib/bel/script.rb +206365 -153577
- data/lib/features.rb +21 -0
- data/lib/libbel.rb +201 -0
- data/lib/util.rb +125 -0
- metadata +190 -43
- checksums.yaml +0 -7
- data/lib/bel/parse_objects.rb +0 -115
data/INSTALL.md
ADDED
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Install
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=======
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This library requires [Ruby](https://www.ruby-lang.org) (**>= 1.9.2**). See [how to install ruby](https://github.com/OpenBEL/bel.rb/blob/master/INSTALL_RUBY.md).
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Install from [RubyGems.org](http://rubygems.org/gems/bel)
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```bash
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gem install bel
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```
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Build from master branch
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1. Obtain source for master branch.
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- `git clone git@github.com:OpenBEL/bel.rb.git`
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2. Build
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- `gem build bel.gemspec`
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- `gem install bel-[VERSION].gem`
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data/INSTALL_RUBY.md
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# Install Ruby
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## Install Ruby (Windows)
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1. Download [RubyInstaller](http://rubyinstaller.org/downloads).
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* Versions 1.9.3 and 2.x.x are supported.
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2. Install RubyInstaller version.
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* Enable the _Add Ruby executables to your PATH_ option presented during installation.
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3. Open a command prompt (Windows Key + R then type `cmd`).
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* Confirm installation by typing `ruby -v`.
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* The output should show the ruby version (e.g. `ruby 2.0.0p451 (2014-02-24) [x64-mingw32]`).
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Continue with <a href="#install_bel_gem">Install the bel gem</a>.
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## Install Ruby (Mac OSX)
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_Option 1: Homebrew_
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1. Install with homebrew by typing `brew install ruby`.
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2. Add ruby commands to your PATH.
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* Add to .bash_profile.
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* `echo 'export PATH="/usr/local/Cellar/ruby/VERSION/bin:$PATH"' >> .bash_profile`
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* Update environment by sourcing .bash_profile.
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* `source ~/.bash_profile`
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3. Confirm installation by typing `ruby -v`.
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_Option 2: rbenv_
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* _Install with homebrew._
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* `brew update`
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* `brew install rbenv ruby-build`
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* More details [here] (https://github.com/sstephenson/rbenv#homebrew-on-mac-os-x).
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* _Install with git._
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* Clone rbenv repository.
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* `git clone https://github.com/sstephenson/rbenv.git ~/.rbenv`
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* Add to .bash_profile.
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* `echo 'export PATH="$HOME/.rbenv/bin:$PATH"' >> ~/.bash_profile`
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* Enable shims and autocompletion from the terminal.
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* `echo 'eval "$(rbenv init -)"' >> ~/.bash_profile`
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* Clone ruby-build repository.
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* `git clone https://github.com/sstephenson/ruby-build.git ~/.rbenv/plugins/ruby-build`
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* More details [here] (https://github.com/sstephenson/rbenv#installation).
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Continue with <a href="#install_bel_gem">Install the bel gem</a>.
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## Install Ruby (Linux)
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_Option 1: Install via package manager._
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* Example installation with Ubuntu.
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* Type `sudo apt-get install ruby` in the terminal.
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_Option 2: rbenv_
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* _Install with git._
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* Clone rbenv repository.
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* `git clone https://github.com/sstephenson/rbenv.git ~/.rbenv`
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* Add to .bash_profile.
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* `echo 'export PATH="$HOME/.rbenv/bin:$PATH"' >> ~/.bash_profile`
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* Enable shims and autocompletion from the terminal.
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* `echo 'eval "$(rbenv init -)"' >> ~/.bash_profile`
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* Clone ruby-build repository.
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* `git clone https://github.com/sstephenson/ruby-build.git ~/.rbenv/plugins/ruby-build`
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* More details [here] (https://github.com/sstephenson/rbenv#installation).
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Continue with <a href="#install_bel_gem">Install the bel gem</a>.
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<br><br>
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<div id="install_bel_gem"></div>
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## Install the _bel_ gem
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1. Open a terminal or command prompt.
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2. Use the `gem` command to install the `bel` gem.
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* `gem install bel`
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3. You should see the following:
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<pre>
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Fetching: bel-0.2.1.gem (100%)
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Successfully installed bel-0.2.1
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Parsing documentation for bel-0.2.1
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Installing ri documentation for bel-0.2.1
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1 gem installed
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</pre>
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4. Confirm you can access the `bel_upgrade` command.
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5. Continue with <a href="#upgrading_bel">Upgrading BEL</a>.
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<br><br>
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<div id="upgrading_bel"></div>
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## Upgrading BEL
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1. Type `bel_upgrade --help` for option details.
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2. Run command
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* Example 1 - convert a BEL file
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* `bel_upgrade --bel small_corpus.bel --changelog "http://resource.belframework.org/belframework/20131211/change_log.json"
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* Example 2 - convert BEL from standard in
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* `curl "http://resource.belframework.org/belframework/1.0/knowledge/small_corpus.bel" | bel_upgrade --changelog "http://resource.belframework.org/belframework/20131211/change_log.json"`
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* More details [here] (https://github.com/OpenBEL/bel.rb).
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3. The upgraded BEL will be written to standard out. Simply redirect to a file after that.
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* `bel_upgrade ... > upgraded-version.bel`
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<br><br>
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## Issues
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* If you have questions with `bel_upgrade` or the `bel` gem please post to the [openbel-discuss] (https://groups.google.com/forum/#!forum/openbel-discuss) google group.
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* If you encounter errors please post an issue to [github issues] (https://github.com/OpenBEL/bel.rb/issues).
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data/README.md
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bel ruby
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========
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[![Gem Version](https://badge.fury.io/rb/bel.svg)](http://badge.fury.io/rb/bel)
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The bel ruby gem allows the reading, writing, and processing of BEL (Biological Expression Language) with a natural DSL.
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Learn more on [BEL](http://www.openbel.org/content/bel-lang-language).
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License: [Apache License, Version 2.0](http://opensource.org/licenses/Apache-2.0)
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Dependencies
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- Required
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- Ruby 1.9.2 or greater ([how to install ruby](INSTALL_RUBY.md))
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- Optional
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- *rdf gem*, *addressable gem*, and *uuid gem* for RDF conversion
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- *rdf-turtle gem* for serializing to RDF turtle format
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Install / Build: See [INSTALL](INSTALL.md).
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branches
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--------
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- master branch
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- [![Travis CI Build](https://travis-ci.org/OpenBEL/bel.rb.svg?branch=master)](https://travis-ci.org/OpenBEL/bel.rb)
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- next branch
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- [![Build Status for next branch](https://travis-ci.org/OpenBEL/bel.rb.svg?branch=next)](https://travis-ci.org/OpenBEL/bel.rb)
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executable commands
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-------------------
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**bel_upgrade**: Upgrade namespaces in BEL content to another version (i.e. *1.0* to *20131211*)
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```bash
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# using BEL file and change log JSON file
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bel_upgrade --bel small_corpus.bel --changelog change_log.json
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# using BEL file and change log from a URL
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bel_upgrade --bel small_corpus.bel --changelog http://resource.belframework.org/belframework/20131211/change_log.json
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# using BEL from STDIN and change log from a URL
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cat small_corpus.bel | bel_upgrade --changelog http://resource.belframework.org/belframework/20131211/change_log.json
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```
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**bel_upgrade_term**: Upgrade BEL terms to another version (e.g. *1.0* to *20131211*)
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```bash
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# using BEL terms and change log JSON file
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bel_upgrade_term -t "p(HGNC:A2LD1)\np(EGID:84)\n" -n "1.0" -c change_log.json
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# using BEL terms and change log from a URL
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bel_upgrade_term -t "p(HGNC:A2LD1)\np(EGID:84)\n" -n "1.0" -c http://resource.belframework.org/belframework/20131211/change_log.json
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# using BEL from STDIN
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echo -e "p(EGID:84)\np(HGNC:A2LD1)" | bel_upgrade_term -n "1.0" -c change_log.json
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cat terms.bel | bel_upgrade_term -n "1.0" -c change_log.json
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```
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**bel_rdfschema**: Dumps the RDF Schema triples for BEL.
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```bash
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# dumps schema in ntriples format (default)
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bel_rdfschema
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# dumps schema in turtle format
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# note: requires the 'rdf-turtle' gem
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bel_rdfschema --format turtle
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```
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**bel2rdf**: Converts BEL to RDF.
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```bash
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# dumps RDF to standard out in ntriples format (default)
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# (from file)
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bel2rdf --bel small_corpus.bel
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# (from standard in)
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cat small_corpus.bel | bel2rdf
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# dumps RDF to standard out in turtle format
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# (from file)
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bel2rdf --bel small_corpus.bel --format turtle
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# (from standard in)
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cat small_corpus.bel | bel2rdf --format turtle
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```
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**bel_parse**: Show parsed objects from BEL content for debugging purposes
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```bash
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# ...from file
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bel_parse --bel small_corpus.bel
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# ...from standard in
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cat small_corpus.bel | bel_parse
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```
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api examples
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------------
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**Use OpenBEL namespaces from the latest release.**
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```ruby
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require 'bel'
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# reference namespace value using standard prefixes (HGNC, MGI, RGD, etc.)
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HGNC['AKT1']
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=> #<BEL::Language::Parameter:0x00000004df5bc0
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@enc=:GRP,
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@ns_def="BEL::Namespace::HGNC",
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@value=:AKT1>
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```
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**Load your own namespace**
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```ruby
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require 'bel'
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# define a NamespaceDefinition with prefix symbol and url
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PUBCHEM = NamespaceDefinition.new(:PUBCHEM, 'http://your-url.org/pubchem.belns')
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# reference caffeine compound, sip, and enjoy
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PUBCHEM['2519']
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```
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**Load namespaces from a published OpenBEL version**
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```ruby
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require 'bel'
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ResourceIndex.openbel_published_index('1.0').namespaces.find { |x| x.prefix == :HGU133P2 }
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ResourceIndex.openbel_published_index('20131211').namespaces.find { |x| x.prefix == :AFFX }
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ResourceIndex.openbel_published_index('latest-release').namespaces.find { |x| x.prefix == :AFFX }
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```
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**Load namespaces from a custom resource index**
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```ruby
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require 'bel'
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ResourceIndex.new('/home/bel/index.xml').namespaces.map(&:prefix)
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=> ["AFFX", "CHEBIID", "CHEBI", "DOID", "DO", "EGID", "GOBPID", "GOBP",
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"GOCCID", "GOCC", "HGNC", "MESHPP", "MESHCS", "MESHD", "MGI", "RGD",
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"SCHEM", "SDIS", "SFAM", "SCOMP", "SPAC", "SP"]
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```
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**Validate BEL parameters**
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```ruby
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require 'bel'
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# AKT1 contained within HGNC NamespaceDefinition
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HGNC[:AKT1].valid?
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=> true
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# not_in_namespace is not contained with HGNC NamespaceDefinition
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HGNC[:not_in_namespace].valid?
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=> false
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# namespace is nil so :some_value MAY exist
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Parameter.new(nil, :some_value).valid?
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=> true
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```
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**Validate BEL terms**
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```ruby
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require 'bel'
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tscript(g(HGNC['AKT1'])).valid?
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=> false
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tscript(g(HGNC['AKT1'])).valid_signatures
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=> []
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tscript(g(HGNC['AKT1'])).invalid_signatures.map(&:to_s)
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=> ["tscript(F:complex)a", "tscript(F:p)a"]
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tscript(p(HGNC['AKT1'])).valid?
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=> true
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tscript(p(HGNC['AKT1'])).valid_signatures.map(&:to_s)
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=> ["tscript(F:p)a"]
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tscript(p(HGNC['AKT1'])).invalid_signatures.map(&:to_s)
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=> ["tscript(F:complex)a"]
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```
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**Write BEL in Ruby with a DSL**
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```ruby
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+
require 'bel'
|
207
|
+
|
208
|
+
# create BEL statements
|
209
|
+
p(HGNC['SKIL']).directlyDecreases tscript(p(HGNC['SMAD3']))
|
210
|
+
bp(GO['response to hypoxia']).increases tscript(p(EGID['7157']))
|
211
|
+
```
|
212
|
+
|
213
|
+
**Parse BEL input**
|
214
|
+
|
215
|
+
```ruby
|
216
|
+
|
217
|
+
require 'bel'
|
218
|
+
|
219
|
+
# example BEL document
|
220
|
+
BEL_SCRIPT = <<-EOF
|
221
|
+
SET DOCUMENT Name = "Spec"
|
222
|
+
SET DOCUMENT Authors = User
|
223
|
+
SET Disease = "Atherosclerosis"
|
224
|
+
path(MESHD:Atherosclerosis)
|
225
|
+
path(Atherosclerosis)
|
226
|
+
bp(GO:"lipid oxidation")
|
227
|
+
p(MGI:Mapkap1) -> p(MGI:Akt1,pmod(P,S,473))
|
228
|
+
path(MESHD:Atherosclerosis) => bp(GO:"lipid oxidation")
|
229
|
+
path(MESHD:Atherosclerosis) =| (p(HGNC:MYC) -> bp(GO:"apoptotic process"))
|
230
|
+
EOF
|
231
|
+
|
232
|
+
# BEL::Script.parse returns BEL::Script::Parser
|
233
|
+
BEL::Script.parse('tscript(p(HGNC:AKT1))')
|
234
|
+
=> #<BEL::Script::Parser:0x007f179261d270>
|
235
|
+
|
236
|
+
# BEL::Script::Parser is Enumerable so we can analyze as we parse
|
237
|
+
# for example: count all function types into a hash
|
238
|
+
BEL::Script.parse('tscript(p(HGNC:AKT1))', {HGNC: HGNC}).find_all { |obj|
|
239
|
+
obj.is_a? Term
|
240
|
+
}.map { |term|
|
241
|
+
term.fx
|
242
|
+
}.reduce(Hash.new {|h,k| h[k] = 0}) { |result, function|
|
243
|
+
result[function.short_form] += 1
|
244
|
+
result
|
245
|
+
}
|
246
|
+
=> {:p=>1, :tscript=>1}
|
247
|
+
|
248
|
+
# parse; yield each parsed object to the block
|
249
|
+
namespace_mapping = {GO: GOBP, HGNC: HGNC, MGI: MGI, MESHD: MESHD}
|
250
|
+
BEL::Script.parse(BEL_SCRIPT, namespace_mapping) do |obj|
|
251
|
+
puts "#{obj.class} #{obj}"
|
252
|
+
end
|
253
|
+
=> BEL::Script::DocumentProperty: SET DOCUMENT Name = "Spec"
|
254
|
+
=> BEL::Script::DocumentProperty: SET DOCUMENT Authors = "User"
|
255
|
+
=> BEL::Script::Annotation: SET Disease = "Atherosclerosis"
|
256
|
+
=> BEL::Script::Parameter: MESHD:Atherosclerosis
|
257
|
+
=> BEL::Script::Term: path(MESHD:Atherosclerosis)
|
258
|
+
=> BEL::Script::Statement: path(MESHD:Atherosclerosis)
|
259
|
+
=> BEL::Script::Parameter: Atherosclerosis
|
260
|
+
=> BEL::Script::Term: path(Atherosclerosis)
|
261
|
+
=> BEL::Script::Statement: path(Atherosclerosis)
|
262
|
+
=> BEL::Script::Parameter: GO:"lipid oxidation"
|
263
|
+
=> BEL::Script::Term: bp(GO:"lipid oxidation")
|
264
|
+
=> BEL::Script::Statement: bp(GO:"lipid oxidation")
|
265
|
+
=> BEL::Script::Parameter: MGI:Mapkap1
|
266
|
+
=> BEL::Script::Term: p(MGI:Mapkap1)
|
267
|
+
=> BEL::Script::Parameter: MGI:Akt1
|
268
|
+
=> BEL::Script::Parameter: P
|
269
|
+
=> BEL::Script::Parameter: S
|
270
|
+
=> BEL::Script::Parameter: 473
|
271
|
+
=> BEL::Script::Term: p(MGI:Akt1,pmod(P,S,473))
|
272
|
+
=> BEL::Script::Statement: p(MGI:Mapkap1) -> p(MGI:Akt1,pmod(P,S,473))
|
273
|
+
=> BEL::Script::Parameter: MESHD:Atherosclerosis
|
274
|
+
=> BEL::Script::Term: path(MESHD:Atherosclerosis)
|
275
|
+
=> BEL::Script::Parameter: GO:"lipid oxidation"
|
276
|
+
=> BEL::Script::Term: bp(GO:"lipid oxidation")
|
277
|
+
=> BEL::Script::Statement: path(MESHD:Atherosclerosis) => bp(GO:"lipid oxidation")
|
278
|
+
=> BEL::Script::Parameter: MESHD:Atherosclerosis
|
279
|
+
=> BEL::Script::Term: path(MESHD:Atherosclerosis)
|
280
|
+
=> BEL::Script::Parameter: HGNC:MYC
|
281
|
+
=> BEL::Script::Term: p(HGNC:MYC)
|
282
|
+
=> BEL::Script::Parameter: GO:"apoptotic process"
|
283
|
+
=> BEL::Script::Term: bp(GO:"apoptotic process")
|
284
|
+
=> BEL::Script::Statement: path(MESHD:Atherosclerosis) =| (p(HGNC:MYC) -> bp(GO:"apoptotic process"))
|
285
|
+
```
|
286
|
+
|
287
|
+
**Iteratively parse BEL from file-like object**
|
288
|
+
|
289
|
+
```ruby
|
290
|
+
|
291
|
+
require 'bel'
|
292
|
+
BEL::Script.parse(File.open('/home/user/small_corpus.bel')).find_all { |obj|
|
293
|
+
obj.is_a? Statement
|
294
|
+
}.to_a.size
|
295
|
+
```
|
296
|
+
|
297
|
+
**Parse BEL and convert to RDF (requires the *rdf*, *addressable*, and *uuid* gems)**
|
298
|
+
|
299
|
+
```ruby
|
300
|
+
|
301
|
+
require 'bel'
|
302
|
+
parser = BEL::Script::Parser.new
|
303
|
+
|
304
|
+
rdf_statements = []
|
305
|
+
|
306
|
+
# parse term
|
307
|
+
parser.parse('p(HGNC:AKT1)') do |obj|
|
308
|
+
if obj.is_a? BEL::Language::Term
|
309
|
+
rdf_statements += obj.to_rdf
|
310
|
+
end
|
311
|
+
end
|
312
|
+
|
313
|
+
# parse statement
|
314
|
+
parser.parse("p(HGNC:AKT1) => tscript(g(HGNC:TNF))\n") do |obj|
|
315
|
+
if obj.is_a? BEL::Language::Statement
|
316
|
+
rdf_statements += obj.to_rdf
|
317
|
+
end
|
318
|
+
end
|
319
|
+
```
|
data/bel.gemspec
ADDED
@@ -0,0 +1,67 @@
|
|
1
|
+
Gem::Specification.new do |spec|
|
2
|
+
spec.name = 'bel'
|
3
|
+
spec.version = '0.3.0.beta1'
|
4
|
+
spec.summary = '''
|
5
|
+
Process BEL with ruby.
|
6
|
+
'''.gsub(%r{^\s+}, ' ').gsub(%r{\n}, '')
|
7
|
+
spec.description = '''
|
8
|
+
The BEL gem allows the reading, writing,
|
9
|
+
and processing of BEL (Biological Expression
|
10
|
+
Language) with a natural DSL.
|
11
|
+
'''.gsub(%r{^\s+}, ' ').gsub(%r{\n}, '')
|
12
|
+
spec.license = 'Apache-2.0'
|
13
|
+
spec.authors = [
|
14
|
+
'Anthony Bargnesi',
|
15
|
+
'Natalie Catlett',
|
16
|
+
'Nick Bargnesi',
|
17
|
+
'William Hayes'
|
18
|
+
]
|
19
|
+
spec.email = [
|
20
|
+
'abargnesi@selventa.com',
|
21
|
+
'ncatlett@selventa.com',
|
22
|
+
'nbargnesi@selventa.com',
|
23
|
+
'whayes@selventa.com'
|
24
|
+
]
|
25
|
+
spec.files = [
|
26
|
+
Dir.glob("lib/**/*.rb"),
|
27
|
+
Dir.glob("ext/**/*.{c,h,def}"),
|
28
|
+
__FILE__,
|
29
|
+
'LICENSE',
|
30
|
+
'INSTALL.md',
|
31
|
+
'INSTALL_RUBY.md',
|
32
|
+
'README.md'
|
33
|
+
].flatten!
|
34
|
+
spec.executables = Dir.glob('bin/*').map(&File.method(:basename))
|
35
|
+
spec.homepage = 'https://github.com/OpenBEL/bel.rb'
|
36
|
+
spec.rdoc_options = [
|
37
|
+
'--title', 'BEL Ruby Documentation',
|
38
|
+
'--main', 'README.md',
|
39
|
+
'--line-numbers',
|
40
|
+
'--exclude', 'lib/bel/script.rb',
|
41
|
+
'README.md',
|
42
|
+
'INSTALL.md',
|
43
|
+
'INSTALL_RUBY.md',
|
44
|
+
'LICENSE'
|
45
|
+
]
|
46
|
+
|
47
|
+
spec.extensions << 'ext/mri/extconf.rb'
|
48
|
+
spec.required_ruby_version = '>= 1.9.2'
|
49
|
+
|
50
|
+
# runtime
|
51
|
+
spec.add_dependency 'ffi', '~> 1.9'
|
52
|
+
|
53
|
+
# test rdf functionality
|
54
|
+
spec.add_development_dependency 'uuid', '~> 2.3'
|
55
|
+
spec.add_development_dependency 'addressable', '~> 2.3'
|
56
|
+
spec.add_development_dependency 'rdf', '~> 1.1'
|
57
|
+
|
58
|
+
# development gems
|
59
|
+
spec.add_development_dependency 'bundler', '~> 1.7'
|
60
|
+
spec.add_development_dependency 'rake', '~> 10.4'
|
61
|
+
spec.add_development_dependency 'rake-compiler', '~> 0.9'
|
62
|
+
spec.add_development_dependency 'rspec', '~> 3.2'
|
63
|
+
spec.add_development_dependency 'yard', '~> 0.8'
|
64
|
+
spec.add_development_dependency 'rdoc', '~> 4.2'
|
65
|
+
end
|
66
|
+
# vim: ts=2 sw=2:
|
67
|
+
# encoding: utf-8
|