pets 0.1.2 → 0.1.3
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- checksums.yaml +4 -4
- data/README.md +8 -6
- data/bin/coPatReporter.rb +1 -1
- data/bin/get_network_nodes.rb +1 -1
- data/bin/paco_translator.rb +1 -1
- data/bin/phen2reg.rb +1 -1
- data/bin/reg2phen.rb +1 -1
- data/lib/pets/version.rb +1 -1
- metadata +2 -2
checksums.yaml
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---
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SHA1:
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metadata.gz:
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data.tar.gz:
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metadata.gz: dd324bc8a0b43977ceab64dd0aa64a4c0200d7d1
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data.tar.gz: f3ba9b874004893503c999bd39e86b8cebbff8fc
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 2cf6fe6377aeb425e57f04712cf913f648acb67050c62b92ffcbf88bffb55f710ed5de071a58b630d3e6abc822c4f6e126b5b7e9f481b352e40128da6aed2091
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data.tar.gz: 543b413cbdbdcbf198514fb195fa5e02027f3fe54ac7ae593a9078402fbb56711f7308aea715582191cd03956bef6f78be5dc5a3d9ff7dd78efb6b698c568670
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data/README.md
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#
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# Pets
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Pets (Patient exploration tools suite) include tools for the analysis of cohorts of patients with pathological phenotypes described in terms of the Human Phenotype Ontology (HPO) and the position their genomic variants clinically determined.
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Pets include tools to (1) perform cohort analysis (coPatReporter.rb), (2) searching for pathological phenotypes associated with a genomic region of interest (reg2phen.rb) and (3) predict regions of the genome that potentially lead to the pathological phenotypes observed in a patient (phen2reg.rb).
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Associations between pathological phenotypes and genomic regions (using genomic coordinates from GRCh37 human assembly) are previously calculated using NetAnalyzer (https://rubygems.org/gems/NetAnalyzer). Please cite us as Rojano E. et al (2017). Revealing the Relationship Between Human Genome Regions and Pathological Phenotypes Through Network Analysis. LNCS, 10208:197-207.
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## Installation
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Add this line to your application's Gemfile:
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```ruby
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gem '
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gem 'pets'
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```
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And then execute:
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Or install it yourself as:
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$ gem install
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$ gem install pets
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## Usage
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@@ -32,7 +34,7 @@ To install this gem onto your local machine, run `bundle exec rake install`. To
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## Contributing
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Bug reports and pull requests are welcome on GitHub at https://
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Bug reports and pull requests are welcome on GitHub at https://bitbucket.org/elenarojano/pets.
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## License
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data/bin/coPatReporter.rb
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@@ -6,7 +6,7 @@ EXTERNAL_DATA = File.expand_path(File.join(ROOT_PATH, '..', 'external_data'))
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HPO_FILE = File.join(EXTERNAL_DATA, 'hp.obo')
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IC_FILE = File.join(EXTERNAL_DATA, 'uniq_hpo_with_CI.txt')
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CHR_SIZE = File.join(EXTERNAL_DATA, 'chromosome_sizes_hg19.txt')
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$: << File.expand_path(File.join(ROOT_PATH, '..', 'lib', '
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$: << File.expand_path(File.join(ROOT_PATH, '..', 'lib', 'pets'))
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require 'optparse'
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require 'csv'
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data/bin/get_network_nodes.rb
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data/bin/paco_translator.rb
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ROOT_PATH = File.dirname(__FILE__)
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EXTERNAL_DATA = File.expand_path(File.join(ROOT_PATH, '..', 'external_data'))
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HPO_FILE = File.join(EXTERNAL_DATA, 'hp.obo')
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$: << File.expand_path(File.join(ROOT_PATH, '..', 'lib', '
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$: << File.expand_path(File.join(ROOT_PATH, '..', 'lib', 'pets'))
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require 'generalMethods.rb'
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require 'optparse'
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data/bin/phen2reg.rb
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REPORT_FOLDER=File.expand_path(File.join(File.dirname(__FILE__), '..', 'templates'))
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ROOT_PATH = File.dirname(__FILE__)
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$: << File.expand_path(File.join(ROOT_PATH, '..', 'lib', '
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$: << File.expand_path(File.join(ROOT_PATH, '..', 'lib', 'pets'))
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require 'net/ftp'
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require 'net/http'
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require 'zlib'
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data/bin/reg2phen.rb
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#data2predict = file to predict
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#training_file.txt = file with training data (association values and hpo codes).
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require 'optparse'
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require File.join(File.dirname(__FILE__), '..', 'lib', '
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require File.join(File.dirname(__FILE__), '..', 'lib', 'pets', 'generalMethods.rb')
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##########################
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#METHODS
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data/lib/pets/version.rb
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metadata
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@@ -1,14 +1,14 @@
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--- !ruby/object:Gem::Specification
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name: pets
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version: !ruby/object:Gem::Version
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version: 0.1.
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version: 0.1.3
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platform: ruby
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authors:
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- Elena Rojano, Pedro Seoane
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autorequire:
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bindir: bin
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cert_chain: []
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date: 2019-10-
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date: 2019-10-28 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: bundler
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