divvy_proteomics 0.3.1 → 0.3.3

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Files changed (6) hide show
  1. checksums.yaml +4 -4
  2. data/README.md +17 -8
  3. data/VERSION +1 -1
  4. data/bin/divvy_spectra +2 -0
  5. data/divvy_proteomics.gemspec +4 -4
  6. metadata +3 -3
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data/README.md CHANGED
@@ -5,20 +5,29 @@ Takes a DTASelect CSV file, and parses the result so non-unique peptides get acc
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  ## Install
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  Get ruby somehow, if you don't already have it. Then, install this gem:
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  ```
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- $ gem install divvy_spectra
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+ $ gem install divvy_proteomics
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+ ```
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+ Or if there is permissions problems e.g. on OSX,
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+ ```
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+ $ sudo gem install divvy_proteomics
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  ```
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  ## Usage
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+ To test it work and to get a full listing of help
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+ ```sh
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+ $ divvy_spectra -h
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  ```
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- $ divvy_spectra <DTASelectFile>
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- ```
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- Output is a table, with a row for each protein with a few columns, including number of unique spectra and the
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- estimated number of spectral counts after sorting out the non-uniqueness. Using the ```--pep-xml``` flag, PepXML files
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- are can be used as input also:
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+ To run on a PepXML file e.g.
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  ```
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- $ divvy_spectra --pep-xml <PepXML_file>
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+ $ divvy_spectra --pep-xml my.pep.xml
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  ```
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+ or a DTASelect file
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+ ```
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+ $ divvy_spectra DTASelect_file
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+ ```
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+ Output is a table, with a row for each protein with a few columns, including number of unique spectra and the
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+ estimated number of spectral counts after sorting out the non-uniqueness.
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  Full usage information:
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  ```
@@ -57,6 +66,6 @@ Verbosity:
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  ## Copyright
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- Copyright (c) 2013 Ben J Woodcroft. See LICENSE.txt for
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+ Copyright (c) 2013-2015 Ben J Woodcroft. See LICENSE.txt for
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  further details.
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data/VERSION CHANGED
@@ -1 +1 @@
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- 0.3.1
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+ 0.3.3
data/bin/divvy_spectra CHANGED
@@ -80,11 +80,13 @@ end
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  # Parse the csv file
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  parsed = nil
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+ log.info "Parsing input.."
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  if options[:input_is_pep_xml]
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  parsed = Bio::PepXML.parse(ARGF)
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  else
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  parsed = Bio::DTASelect::OutputFile.parse(ARGF)
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  end
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+ log.info "Finished parsing"
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  # Hashes of identifiers to objects
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  proteins = parsed.protein_name_to_object
data/divvy_proteomics.gemspec CHANGED
@@ -2,16 +2,16 @@
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  # DO NOT EDIT THIS FILE DIRECTLY
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  # Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
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  # -*- encoding: utf-8 -*-
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- # stub: divvy_proteomics 0.3.1 ruby lib
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+ # stub: divvy_proteomics 0.3.3 ruby lib
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  Gem::Specification.new do |s|
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  s.name = "divvy_proteomics"
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- s.version = "0.3.1"
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+ s.version = "0.3.3"
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  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
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  s.require_paths = ["lib"]
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  s.authors = ["Ben J Woodcroft"]
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- s.date = "2014-01-07"
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+ s.date = "2015-02-20"
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  s.description = "divvy up spectra from DTASelect files in a somewhat parsimonious way"
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  s.email = "donttrustben@gmail.com"
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  s.executables = ["divvy_spectra"]
@@ -52,7 +52,7 @@ Gem::Specification.new do |s|
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  ]
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  s.homepage = "http://github.com/wwood/divvy_proteomics"
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  s.licenses = ["MIT"]
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- s.rubygems_version = "2.2.0"
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+ s.rubygems_version = "2.2.2"
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  s.summary = "divvy up spectra from DTASelect files in a parsimonious way"
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  if s.respond_to? :specification_version then
metadata CHANGED
@@ -1,14 +1,14 @@
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  --- !ruby/object:Gem::Specification
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  name: divvy_proteomics
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  version: !ruby/object:Gem::Version
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- version: 0.3.1
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+ version: 0.3.3
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  platform: ruby
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  authors:
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  - Ben J Woodcroft
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  autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2014-01-07 00:00:00.000000000 Z
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+ date: 2015-02-20 00:00:00.000000000 Z
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  dependencies:
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  - !ruby/object:Gem::Dependency
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  name: bio-logger
@@ -152,7 +152,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
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  version: '0'
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  requirements: []
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  rubyforge_project:
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- rubygems_version: 2.2.0
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+ rubygems_version: 2.2.2
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  signing_key:
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  specification_version: 4
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  summary: divvy up spectra from DTASelect files in a parsimonious way