genomer-plugin-summary 0.0.4 → 0.0.5

data/README.md

@@ -1,29 +1,67 @@
-# Genomer::Plugin::Summary
+![Summary: metrics for genome projects](http://genomer.s3.amazonaws.com/icon/summary/summary.jpg)
 
-TODO: Write a gem description
+## About
+
+Summary is a plugin for the [genomer][] tool for genome finishing. This summary
+plugin provides metrics that useful are to understanding that state of your
+genome scaffold. Plugins are added to a genomer project by specifying them in
+the project Gemfile. Each summary function is documented with a [manual
+page][man].
+
+[genomer]: https://github.com/michaelbarton/genomer
+[man]: https://github.com/michaelbarton/genomer-plugin-summary/tree/master/man
+
+## Usage
+
+The following command will provide a list of all the gaps in your genome
+scaffold:
+
+    $ genomer summary gaps
+
+Producing output similiar to as follows:
+
+    +----------+----------+----------+----------+--------------+
+    |                      Scaffold Gaps                       |
+    +----------+----------+----------+----------+--------------+
+    |  Number  |  Length  |  Start   |   End    |     Type     |
+    +----------+----------+----------+----------+--------------+
+    |        1 |      400 |   121250 |   121649 |  unresolved  |
+    |        2 |      659 |   123354 |   124012 |    contig    |
+    |        3 |       10 |   126781 |   126790 |  unresolved  |
+    |        4 |       10 |   127393 |   127402 |  unresolved  |
+    |        5 |      500 |   778936 |   779435 |  unresolved  |
+    |        6 |      659 |   781140 |   781798 |    contig    |
+    |        7 |       10 |   784567 |   784576 |  unresolved  |
+    |        8 |      300 |   785179 |   785478 |  unresolved  |
+    |        9 |      556 |   803968 |   804523 |    contig    |
+    |       10 |      242 |  1032294 |  1032535 |    contig    |
+    |       11 |     1751 |  1057108 |  1058858 |    contig    |
+    |       12 |      575 |  1137194 |  1137768 |    contig    |
+    <remainder omitted>
+
+Other commands are available for showing contigs, sequences, and the complete
+scaffolded genome. These are listed in the [manual page][man] directory.
 
 ## Installation
 
-Add this line to your application's Gemfile:
+Add this line to your genomer projects's Gemfile:
 
     gem 'genomer-plugin-summary'
 
-And then execute:
+And then execute in the project directory:
 
     $ bundle
 
-Or install it yourself as:
+Run the `help` command and the summary plugin should be available:
 
-    $ gem install genomer-plugin-summary
-
-## Usage
+    $ genomer help
+    $ genomer man summary
 
-TODO: Write usage instructions here
+## Copyright
 
-## Contributing
+Genomer copyright (c) 2010 by Michael Barton. Genomer is licensed under the MIT
+license. See LICENSE.txt for further details. The tape measure image is used
+under a Creative Commons Generic 2.0 Licence. The original can be [found on
+flickr.][flickr]
 
-1. Fork it
-2. Create your feature branch (`git checkout -b my-new-feature`)
-3. Commit your changes (`git commit -am 'Added some feature'`)
-4. Push to the branch (`git push origin my-new-feature`)
-5. Create new Pull Request
+[flickr]: http://www.flickr.com/photos/aussiegall/286709039/

data/VERSION

@@ -1 +1 @@
-0.0.4
+0.0.5

data/features/contigs.feature

@@ -1,7 +1,15 @@
 Feature: Producing a summary of the scaffold contigs
   In order to have an overview of the contigs in a scaffold
   A user can use the "contigs" command
-  to generate the a tabular output of the scaffold contigs
+  to generate a tabular output of the scaffold contigs
+
+  @disable-bundler
+  Scenario: Getting the man page for the scaffold contigs summary
+    Given I create a new genomer project
+     When I run `genomer man summary contigs`
+     Then the exit status should be 0
+      And the output should contain a valid man page
+      And the output should contain "GENOMER-SUMMARY-CONTIGS(1)"
 
   @disable-bundler
   Scenario: An empty scaffold

data/features/core.feature

@@ -0,0 +1,13 @@
+Feature: Producing different summaries of a genomes scaffold
+  In order to have an overview of a genome scaffold
+  A user can use the "summary" plugin
+  to generate different tabular output of the scaffold
+
+  @disable-bundler
+  Scenario: Getting the man page for the scaffold summary plugin
+    Given I create a new genomer project
+     When I run `genomer man summary`
+     Then the exit status should be 0
+      And the output should contain a valid man page
+      And the output should contain "GENOMER-SUMMARY(1)"
+      And the output should contain "gaps"

data/features/gaps.feature

@@ -1,7 +1,15 @@
 Feature: Producing a summary of the scaffold gaps
   In order to have an overview of the gaps in a scaffold
   A user can use the "gaps" command
-  to generate the a tabular output of the scaffold gaps
+  to generate a tabular output of the scaffold gaps
+
+  @disable-bundler
+  Scenario: Getting the man page for the scaffold gaps summary
+    Given I create a new genomer project
+     When I run `genomer man summary gaps`
+     Then the exit status should be 0
+      And the output should contain a valid man page
+      And the output should contain "GENOMER-SUMMARY-GAPS(1)"
 
   @disable-bundler
   Scenario: A single contig scaffold

data/features/genome.feature

@@ -1,7 +1,15 @@
 Feature: Producing a summary of the genome
   In order to have an overview of the genome
   A user can use the "genome" command
-  to generate the a tabular output of the genome
+  to generate a tabular output of the genome
+
+  @disable-bundler
+  Scenario: Getting the man page for the scaffold genome summary
+    Given I create a new genomer project
+     When I run `genomer man summary genome`
+     Then the exit status should be 0
+      And the output should contain a valid man page
+      And the output should contain "GENOMER-SUMMARY-GENOME(1)"
 
   Scenario: A scaffold with a single sequence
     Given I create a new genomer project

data/features/sequences.feature

@@ -1,7 +1,15 @@
 Feature: Producing a summary of the scaffold sequences
   In order to have an overview of the sequences in a scaffold
   A user can use the "sequence" command
-  to generate the a tabular output of the scaffold sequences
+  to generate a tabular output of the scaffold sequences
+
+  @disable-bundler
+  Scenario: Getting the man page for the scaffold sequences summary
+    Given I create a new genomer project
+     When I run `genomer man summary sequences`
+     Then the exit status should be 0
+      And the output should contain a valid man page
+      And the output should contain "GENOMER-SUMMARY-SEQUENCES(1)"
 
   @disable-bundler
   Scenario: An empty scaffold

data/features/support/genomer_steps.rb

@@ -3,3 +3,9 @@ When /^I create a new genomer project$/ do
   step 'I cd to "project"'
   step 'I append to "Gemfile" with "gem \'genomer-plugin-summary\', :path =>\'../../../\'"'
 end
+
+Then /^the output should contain a valid man page$/ do
+  step 'the output should not contain "md2man/roff: raw_html not implemented"'
+  step 'the output should not contain "\<"'
+  step 'the output should not contain "\>"'
+end

data/man/genomer-summary-contigs.ronn

@@ -0,0 +1,53 @@
+# GENOMER-SUMMARY-CONTIGS 1
+
+## NAME
+
+genomer-summary-contigs(1) -- summarise the contigs in the scaffold
+
+## SYNOPSIS
+
+`genomer summary contigs [<--output=csv>]`
+
+## DESCRIPTION
+
+Generates a summary of the contigous sequence used in the scaffolded output
+sequence. The output may be generated in CSV format if preferred using the
+<--output=csv> option. This summary produces a table with the following
+attributes:
+
+  * Contig:
+
+    The number of the contig in the final scaffold. Generated from counting
+    each contiguous length of non-N characters from the beginning scaffolded
+    sequence.
+
+  * Start:
+
+    The start position of the contig in the final scaffold sequence.
+
+  * End:
+
+    The end position of the contig in the final scaffold sequence.
+
+  * Size (bp):
+
+    The size of the contig in the final scaffold sequence.
+
+  * Size (%):
+
+    The size of the contig in the final scaffold sequence as a percentage of
+    the total sequence.
+
+  * GC:
+
+    The G+C content of the contig as percentage the total GCAT length of the
+    contig.
+
+## BUGS
+
+**Genomer-summary** is written in Ruby and uses several RubyGem dependencies. 
+See the .gemspec file in the install directory for version details.
+
+## COPYRIGHT
+
+**Genomer** is Copyright (C) 2011 Michael Barton <http://michaelbarton.me.uk>

data/man/genomer-summary-gaps.ronn

@@ -1,15 +1,19 @@
+# GENOMER-SUMMARY-GAPS 1
+
+## NAME
+
 genomer-summary-gaps(1) -- summarise the gaps in the scaffold
-=============================================================
 
 ## SYNOPSIS
 
-`genomer summary gaps`
+`genomer summary gaps [<--output=csv>]`
 
 ## DESCRIPTION
 
 Generates a summary of the gaps (regions of N characters) in the scaffolded 
-output sequence. This summary command lists these gaps with the following 
-attributes:
+output sequence. The output may be generated in CSV format if preferred using
+the <--output=csv> option. This summary command lists these gaps with the
+following attributes:
 
   * Number:
     Incremental gap number from the start of the sequence.

data/man/genomer-summary-genome.ronn

@@ -0,0 +1,37 @@
+# GENOMER-SUMMARY-GENOME 1
+
+## NAME
+
+genomer-summary-genome(1) -- summarise the genome scaffold
+
+## SYNOPSIS
+
+`genomer summary genome [<--output=csv>]`
+
+## DESCRIPTION
+
+Generates a summary of the genome scaffold. This summary contains various
+metrics of the scaffold. The output may be generated in CSV format if preferred
+using the <--output=csv> option. This summary produces a table with the
+following attributes:
+
+  * Sequences:
+
+    The sequences used to build the scaffold.
+
+  * Contigs:
+
+    Regions of contiguous non-N characters in the final scaffold sequence.
+
+  * Gaps:
+
+    Regions of contiguous N characters in the final scaffold sequence.
+
+## BUGS
+
+**Genomer-summary** is written in Ruby and uses several RubyGem dependencies. 
+See the .gemspec file in the install directory for version details.
+
+## COPYRIGHT
+
+**Genomer** is Copyright (C) 2011 Michael Barton <http://michaelbarton.me.uk>

data/man/genomer-summary-sequences.ronn

@@ -0,0 +1,50 @@
+# GENOMER-SUMMARY-SEQUENCES 1
+
+## NAME
+
+genomer-summary-sequences(1) -- summarise the sequences in the scaffold
+
+## SYNOPSIS
+
+`genomer summary sequences [<--output=csv>]`
+
+## DESCRIPTION
+
+Generates a summary of the sequences used to build the scaffold. The
+output may be generated in CSV format if preferred using the <--output=csv>
+option. This summary produces a table with the following attributes:
+
+  * Contig:
+
+    The identifier of the sequence in the scaffold.
+
+  * Start:
+
+    The start position of the sequence in the final scaffold sequence.
+
+  * End:
+
+    The end position of the sequence in the final scaffold sequence.
+
+  * Size (bp):
+
+    The size of the sequence in the final scaffold sequence.
+
+  * Size (%):
+
+    The size of the sequence in the final scaffold sequence as a percentage of
+    the total sequence.
+
+  * GC:
+
+    The G+C content of the sequence as percentage the total GCAT length of the
+    sequence.
+
+## BUGS
+
+**Genomer-summary** is written in Ruby and uses several RubyGem dependencies. 
+See the .gemspec file in the install directory for version details.
+
+## COPYRIGHT
+
+**Genomer** is Copyright (C) 2011 Michael Barton <http://michaelbarton.me.uk>

data/man/genomer-summary.ronn

@@ -1,9 +1,12 @@
+# GENOMER-SUMMARY 1
+
+## NAME
+
 genomer-summary(1) -- generate summaries of genomer projects
-============================================================
 
 ## SYNOPSIS
 
-`genomer summary` <summary-type> [<options>...]
+`genomer summary` \<summary-type\> [\<options\>...]
 
 ## DESCRIPTION
 

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: genomer-plugin-summary
 version: !ruby/object:Gem::Version
-  version: 0.0.4
+  version: 0.0.5
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-10-31 00:00:00.000000000 Z
+date: 2013-01-22 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: genomer
@@ -169,6 +169,7 @@ files:
 - Rakefile
 - VERSION
 - features/contigs.feature
+- features/core.feature
 - features/gaps.feature
 - features/genome.feature
 - features/sequences.feature
@@ -183,7 +184,10 @@ files:
 - lib/genomer-plugin-summary/genome.rb
 - lib/genomer-plugin-summary/metrics.rb
 - lib/genomer-plugin-summary/sequences.rb
+- man/genomer-summary-contigs.ronn
 - man/genomer-summary-gaps.ronn
+- man/genomer-summary-genome.ronn
+- man/genomer-summary-sequences.ronn
 - man/genomer-summary.ronn
 - spec/genomer-plugin-summary_spec.rb
 - spec/genomer-plugin-summary_spec/contigs_spec.rb
@@ -208,7 +212,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: 2735699573861550577
+      hash: 2140050632096310214
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements:
@@ -217,7 +221,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: 2735699573861550577
+      hash: 2140050632096310214
 requirements: []
 rubyforge_project: 
 rubygems_version: 1.8.23
@@ -226,6 +230,7 @@ specification_version: 3
 summary: Generates reports on the status of the genomer project
 test_files:
 - features/contigs.feature
+- features/core.feature
 - features/gaps.feature
 - features/genome.feature
 - features/sequences.feature