ecf_classify 1.0.2 → 1.0.3

checksums.yaml

@@ -1,7 +1,7 @@
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data/README.md

@@ -2,9 +2,20 @@
 
 [![Gem Version](https://badge.fury.io/rb/ecf_classify.svg)](https://badge.fury.io/rb/ecf_classify)
 
-Welcome to your new gem! In this directory, you'll find the files you need to be able to package up your Ruby library into a gem. Put your Ruby code in the file `lib/ecf_classify`. To experiment with that code, run `bin/console` for an interactive prompt.
+A small software pipeline for the discovery of potentially new ECF σ factors and the prediction of their functionality with regards to the new classification schema [Casas-Pastor et al.](https://doi.org/10.1093/nar/gkaa1229)
 
-TODO: Delete this and the text above, and describe your gem
+## Prerequisite
+
+Please install [hmmer 3](http://hmmer.org/documentation.html).
+Furthermore, you need to install the following python packages
+
+```
+# requirements.txt
+numpy
+biopython==1.78
+```
+
+`python3 -m pip install -r requirements.txt`
 
 ## Installation
 
@@ -79,13 +90,18 @@ Classifies protein sequences into ECF subgroups
 
 After checking out the repo, run `bin/setup` to install dependencies. Then, run `rake spec` to run the tests. You can also run `bin/console` for an interactive prompt that will allow you to experiment.
 
---> This will not be done before submission
 To install this gem onto your local machine, run `bundle exec rake install`. To release a new version, update the version number in `version.rb`, and then run `bundle exec rake release`, which will create a git tag for the version, push git commits and tags, and push the `.gem` file to [rubygems.org](https://rubygems.org).
 
 ## Contributing
 
 Bug reports and pull requests are welcome on GitHub at https://github.com/r-mllr/ecf_classify.
 
+## Publication / How to cite
+
+Please cite:
+
+Casas-Pastor D, Müller RR, Jaenicke S, Brinkrolf K, Becker A, Buttner MJ, Gross CA, Mascher T, Goesmann A, Fritz G. Expansion and re-classification of the extracytoplasmic function (ECF) σ factor family. Nucleic Acids Res. 2021 Jan 4:gkaa1229. doi: 10.1093/nar/gkaa1229. Epub ahead of print. PMID: 33398323.
+
 ## License
 
 The gem is available as open source under the terms of the [GPL-3](https://opensource.org/licenses/GPL-3.0).

data/cucumber.yml

@@ -0,0 +1 @@
+default: --publish-quiet

data/ecf_classify.gemspec

@@ -24,7 +24,7 @@ Gem::Specification.new do |spec|
   spec.require_paths = ["lib"]
 
   spec.add_development_dependency "bundler", "~> 2.0"
-  spec.add_development_dependency "rake", "~> 10.0"
+  spec.add_development_dependency "rake", ">= 12.3.3"
   spec.add_development_dependency "rspec", "~> 3.0"
   spec.add_development_dependency "aruba", "~> 0.14"
 

data/lib/ecf_classify.rb

@@ -55,6 +55,11 @@ module EcfClassify
       EcfClassify::Zenodo.download
     end
 
+    desc "cite", "How to cite"
+    def cite
+      puts "Thank you for using #{EcfClassify::NAME} in version #{EcfClassify::VERSION}.\nPlease cite \n\n#{EcfClassify::CITE}\n\nif you are using #{EcfClassify::NAME}"
+    end
+
     no_commands do
       def handle_help_option(method_name)
         if options[:help]

data/lib/ecf_classify/version.rb

@@ -1,4 +1,5 @@
 module EcfClassify
-  VERSION = "1.0.2"
+  VERSION = '1.0.3'
   NAME = 'ecf_classify'
+  CITE = 'Casas-Pastor D, Müller RR, Jaenicke S, Brinkrolf K, Becker A, Buttner MJ, Gross CA, Mascher T, Goesmann A, Fritz G. Expansion and re-classification of the extracytoplasmic function (ECF) σ factor family. Nucleic Acids Res. 2021 Jan 4:gkaa1229. doi: 10.1093/nar/gkaa1229. Epub ahead of print. PMID: 33398323.'
 end

data/lib/ecf_classify/zenodo.rb

@@ -21,7 +21,7 @@ module EcfClassify
  ## returns
  ##   true if everything is ok
     def self.download
-      perma_record = open(RECORD_URL)
+      perma_record = URI.open(RECORD_URL)
       FILES.each do |key,file|
         download = open(perma_record.base_uri.to_s + "/files/" + file)
         IO.copy_stream(download, path(key))

data/requirements.txt

@@ -1,2 +1,2 @@
 numpy
-biopython==1.73
+biopython==1.78

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: ecf_classify
 version: !ruby/object:Gem::Version
-  version: 1.0.2
+  version: 1.0.3
 platform: ruby
 authors:
 - Delia Casas Pastor
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: exe
 cert_chain: []
-date: 2020-02-19 00:00:00.000000000 Z
+date: 2021-01-18 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
@@ -29,16 +29,16 @@ dependencies:
   name: rake
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ">="
       - !ruby/object:Gem::Version
-        version: '10.0'
+        version: 12.3.3
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ">="
       - !ruby/object:Gem::Version
-        version: '10.0'
+        version: 12.3.3
 - !ruby/object:Gem::Dependency
   name: rspec
   requirement: !ruby/object:Gem::Requirement
@@ -103,6 +103,7 @@ files:
 - Rakefile.prod
 - bin/console
 - bin/setup
+- cucumber.yml
 - data/.keep
 - ecf_classify.gemspec
 - exe/ecf_classify
@@ -134,7 +135,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.0.3
+rubygems_version: 3.1.4
 signing_key: 
 specification_version: 4
 summary: Gem for installing and running the ECF classify tool