divvy_proteomics 0.3.1 → 0.3.3
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- checksums.yaml +4 -4
- data/README.md +17 -8
- data/VERSION +1 -1
- data/bin/divvy_spectra +2 -0
- data/divvy_proteomics.gemspec +4 -4
- metadata +3 -3
checksums.yaml
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SHA1:
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metadata.gz:
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metadata.gz: d61774af8a5bbd61fd95862de177b2a133d74538
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data.tar.gz: ed3dc902ac58437f328e177c91229423b000b5e7
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SHA512:
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metadata.gz:
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data.tar.gz: 85d9437f116c4092cc0458ccd53b13076b4b25133e398216611fc9255d27870d8a43c8ae66ae34e617c859a79feeeda7c603b49088574d32ef4e7f2639ff72e3
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data/README.md
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@@ -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
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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
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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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```
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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
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1
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0.3.
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0.3.3
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data/bin/divvy_spectra
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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
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data/divvy_proteomics.gemspec
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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.
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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.
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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 = "
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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"]
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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.
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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
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metadata
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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.
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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:
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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
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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.
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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
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