dirseq 0.4.1 → 0.4.3

checksums.yaml

@@ -1,7 +1,7 @@
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data/Gemfile

@@ -11,7 +11,7 @@ gem "bio", "~>1.4", ">=1.4.2"
 group :development do
   #gem "shoulda", "~> 3.5"
   #gem "simplecov", "~> 0.8"
-  gem "jeweler", "~> 2.3"
+  gem "juwelier", "~> 2.4", ">=2.4.9"
   gem "bundler", "~> 2.1"
   gem "rspec", "~> 3.0"
   gem 'pry', '~>0.10'

data/README.md

@@ -8,18 +8,34 @@ Note: this software is under active development!
 
 ## Installation
 
-Won't work just yet:
+Install some prerequisites via conda, and then dirseq itself:
 ```sh
+conda create -c bioconda -n dirseq -y ruby samtools bedtools'>'2.24
+conda activate dirseq
 gem install dirseq
 ```
-Requires:
+
+The following dependencies are installed above, but for completeness of documentation, dirseq requires these dependencies, on top of the Ruby ones:
 * samtools (tested with 0.1.19 and 1.0+)
 * bedtools (tested with 2.24.0) - old versions won't work.
 * Ruby (tested with 2.1.1)
 
 ## Usage
 
-Only the script is available at the moment
+Example usage:
+
+Download the example data:
+```sh
+git clone https://github.com/wwood/dirseq
+cd dirseq
+```
+
+Then run dirseq:
+```sh
+dirseq --bam spec/data/eg.bam --gff spec/data/eg.gff --measure-type count
+```
+
+Full usage help:
 ```sh
 $ dirseq -h
 
@@ -38,6 +54,7 @@ Optional parameters:
         --accepted-feature-types TYPE
                                      Print only features of these type(s) [default CDS]
         --comment-fields             Print elements from the comments in the GFF file [default ID]
+        --sam-filter-flags           Apply these samtools filters [default: -F0x100 -F0x800]
         
 Verbosity:
 
@@ -46,6 +63,11 @@ Verbosity:
         --trace options              Set log level [default INFO]. e.g. '--trace debug' to set logging level to DEBUG
 ```
 
+Running on [EnrichM](https://github.com/geronimp/enrichM) output, the output columns are changed relative to [PROKKA](https://github.com/tseemann/prokka)-generated GFF files:
+```sh
+dirseq --bam spec/data/eg.bam --gff spec/data/eg.gff --measure-type count --comment-fields seq_id,annotations
+```
+
 ## Project home page
 
 Information on the source tree, documentation, examples, issues and
@@ -57,16 +79,11 @@ The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
 
 ## Cite
 
-If you use this software, please cite one of
-
-* [BioRuby: bioinformatics software for the Ruby programming language](http://dx.doi.org/10.1093/bioinformatics/btq475)
-* [Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics](http://dx.doi.org/10.1093/bioinformatics/bts080)
-
-## Biogems.info
+If you use this software, please cite
 
-This Biogem is published at (http://biogems.info/index.html#bio-rnaseq_transcription_directionality)
+Woodcroft, B.J., Singleton, C.M., Boyd, J.A. et al. Genome-centric view of carbon processing in thawing permafrost. Nature 560, 49–54 (2018). https://doi.org/10.1038/s41586-018-0338-1
 
 ## Copyright
 
-Copyright (c) 2014 Ben J. Woodcroft. See LICENSE.txt for further details.
+Copyright (c) 2014-2021 Ben J. Woodcroft. See LICENSE.txt for further details.
 

data/Rakefile

@@ -11,8 +11,8 @@ rescue Bundler::BundlerError => e
 end
 require 'rake'
 
-require 'jeweler'
-Jeweler::Tasks.new do |gem|
+require 'juwelier'
+Juwelier::Tasks.new do |gem|
   # gem is a Gem::Specification... see http://guides.rubygems.org/specification-reference/ for more options
   gem.name = "dirseq"
   gem.homepage = "http://github.com/wwood/dirseq"
@@ -23,7 +23,7 @@ Jeweler::Tasks.new do |gem|
   gem.authors = ["Ben J. Woodcroft"]
   # dependencies defined in Gemfile
 end
-Jeweler::RubygemsDotOrgTasks.new
+Juwelier::RubygemsDotOrgTasks.new
 
 require 'rspec/core'
 require 'rspec/core/rake_task'

data/VERSION

@@ -1 +1 @@
-0.4.1
+0.4.3

data/bin/dirseq

@@ -54,7 +54,7 @@ o = OptionParser.new do |opts|
           "Print only features of these type(s) [default #{options[:accepted_feature_types].join(',')}]") do |arg|
     options[:accepted_feature_types] = Set.new(arg)
   end
-  opts.on("--comment-fields", Array,
+  opts.on("--comment-fields COMMA_SEPARATED_FIELDS", Array,
           "Print elements from the comments in the GFF file [default #{options[:comment_fields_to_print].join(',')}]") do |arg|
     options[:comment_fields_to_print] = arg
   end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: dirseq
 version: !ruby/object:Gem::Version
-  version: 0.4.1
+  version: 0.4.3
 platform: ruby
 authors:
 - Ben J. Woodcroft
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2020-12-14 00:00:00.000000000 Z
+date: 2021-03-08 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio-commandeer
@@ -59,19 +59,25 @@ dependencies:
       - !ruby/object:Gem::Version
         version: 1.4.2
 - !ruby/object:Gem::Dependency
-  name: jeweler
+  name: juwelier
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '2.3'
+        version: '2.4'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 2.4.9
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '2.3'
+        version: '2.4'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 2.4.9
 - !ruby/object:Gem::Dependency
   name: bundler
   requirement: !ruby/object:Gem::Requirement