--- !ruby/object:Gem::Specification
name: mspire
version: !ruby/object:Gem::Version
  version: 0.10.7
platform: ruby
authors:
- John T. Prince
- Simon Chiang
autorequire: 
bindir: bin
cert_chain: []
date: 2014-03-07 00:00:00.000000000 Z
dependencies:
- !ruby/object:Gem::Dependency
  name: nokogiri
  requirement: !ruby/object:Gem::Requirement
    requirements:
    - - "~>"
      - !ruby/object:Gem::Version
        version: 1.6.1
  type: :runtime
  prerelease: false
  version_requirements: !ruby/object:Gem::Requirement
    requirements:
    - - "~>"
      - !ruby/object:Gem::Version
        version: 1.6.1
- !ruby/object:Gem::Dependency
  name: bsearch
  requirement: !ruby/object:Gem::Requirement
    requirements:
    - - ">="
      - !ruby/object:Gem::Version
        version: 1.5.0
  type: :runtime
  prerelease: false
  version_requirements: !ruby/object:Gem::Requirement
    requirements:
    - - ">="
      - !ruby/object:Gem::Version
        version: 1.5.0
- !ruby/object:Gem::Dependency
  name: andand
  requirement: !ruby/object:Gem::Requirement
    requirements:
    - - ">="
      - !ruby/object:Gem::Version
        version: 1.3.3
  type: :runtime
  prerelease: false
  version_requirements: !ruby/object:Gem::Requirement
    requirements:
    - - ">="
      - !ruby/object:Gem::Version
        version: 1.3.3
- !ruby/object:Gem::Dependency
  name: obo
  requirement: !ruby/object:Gem::Requirement
    requirements:
    - - ">="
      - !ruby/object:Gem::Version
        version: 0.1.4
  type: :runtime
  prerelease: false
  version_requirements: !ruby/object:Gem::Requirement
    requirements:
    - - ">="
      - !ruby/object:Gem::Version
        version: 0.1.4
- !ruby/object:Gem::Dependency
  name: builder
  requirement: !ruby/object:Gem::Requirement
    requirements:
    - - "~>"
      - !ruby/object:Gem::Version
        version: 3.2.2
  type: :runtime
  prerelease: false
  version_requirements: !ruby/object:Gem::Requirement
    requirements:
    - - "~>"
      - !ruby/object:Gem::Version
        version: 3.2.2
- !ruby/object:Gem::Dependency
  name: bio
  requirement: !ruby/object:Gem::Requirement
    requirements:
    - - "~>"
      - !ruby/object:Gem::Version
        version: 1.4.3.0001
  type: :runtime
  prerelease: false
  version_requirements: !ruby/object:Gem::Requirement
    requirements:
    - - "~>"
      - !ruby/object:Gem::Version
        version: 1.4.3.0001
- !ruby/object:Gem::Dependency
  name: trollop
  requirement: !ruby/object:Gem::Requirement
    requirements:
    - - "~>"
      - !ruby/object:Gem::Version
        version: 2.0.0
  type: :runtime
  prerelease: false
  version_requirements: !ruby/object:Gem::Requirement
    requirements:
    - - "~>"
      - !ruby/object:Gem::Version
        version: 2.0.0
- !ruby/object:Gem::Dependency
  name: bundler
  requirement: !ruby/object:Gem::Requirement
    requirements:
    - - "~>"
      - !ruby/object:Gem::Version
        version: 1.5.1
  type: :development
  prerelease: false
  version_requirements: !ruby/object:Gem::Requirement
    requirements:
    - - "~>"
      - !ruby/object:Gem::Version
        version: 1.5.1
- !ruby/object:Gem::Dependency
  name: rake
  requirement: !ruby/object:Gem::Requirement
    requirements:
    - - ">="
      - !ruby/object:Gem::Version
        version: '0'
  type: :development
  prerelease: false
  version_requirements: !ruby/object:Gem::Requirement
    requirements:
    - - ">="
      - !ruby/object:Gem::Version
        version: '0'
- !ruby/object:Gem::Dependency
  name: rspec
  requirement: !ruby/object:Gem::Requirement
    requirements:
    - - "~>"
      - !ruby/object:Gem::Version
        version: 2.14.1
  type: :development
  prerelease: false
  version_requirements: !ruby/object:Gem::Requirement
    requirements:
    - - "~>"
      - !ruby/object:Gem::Version
        version: 2.14.1
- !ruby/object:Gem::Dependency
  name: rdoc
  requirement: !ruby/object:Gem::Requirement
    requirements:
    - - "~>"
      - !ruby/object:Gem::Version
        version: 4.1.0
  type: :development
  prerelease: false
  version_requirements: !ruby/object:Gem::Requirement
    requirements:
    - - "~>"
      - !ruby/object:Gem::Version
        version: 4.1.0
- !ruby/object:Gem::Dependency
  name: simplecov
  requirement: !ruby/object:Gem::Requirement
    requirements:
    - - "~>"
      - !ruby/object:Gem::Version
        version: 0.8.2
  type: :development
  prerelease: false
  version_requirements: !ruby/object:Gem::Requirement
    requirements:
    - - "~>"
      - !ruby/object:Gem::Version
        version: 0.8.2
- !ruby/object:Gem::Dependency
  name: coveralls
  requirement: !ruby/object:Gem::Requirement
    requirements:
    - - ">="
      - !ruby/object:Gem::Version
        version: '0'
  type: :development
  prerelease: false
  version_requirements: !ruby/object:Gem::Requirement
    requirements:
    - - ">="
      - !ruby/object:Gem::Version
        version: '0'
- !ruby/object:Gem::Dependency
  name: fftw3
  requirement: !ruby/object:Gem::Requirement
    requirements:
    - - "~>"
      - !ruby/object:Gem::Version
        version: '0.3'
  type: :development
  prerelease: false
  version_requirements: !ruby/object:Gem::Requirement
    requirements:
    - - "~>"
      - !ruby/object:Gem::Version
        version: '0.3'
description: mass spectrometry proteomics, lipidomics, and tools, a rewrite of mspire,
  merging of ms-* gems
email:
- jtprince@gmail.com
executables:
- mspire
extensions: []
extra_rdoc_files: []
files:
- ".gitignore"
- ".travis.yml"
- Gemfile
- LICENSE
- README.md
- Rakefile
- bin/mspire
- lib/core_ext/array/in_groups.rb
- lib/core_ext/enumerable.rb
- lib/cv.rb
- lib/cv/param.rb
- lib/cv/referenceable_param_group_ref.rb
- lib/hash/inverse.rb
- lib/io/bookmark.rb
- lib/merge.rb
- lib/mspire.rb
- lib/mspire/bin.rb
- lib/mspire/commandline.rb
- lib/mspire/cv/obo.rb
- lib/mspire/cv/param.rb
- lib/mspire/cv/paramable.rb
- lib/mspire/digester.rb
- lib/mspire/error_rate/decoy.rb
- lib/mspire/error_rate/qvalue.rb
- lib/mspire/fasta.rb
- lib/mspire/ident.rb
- lib/mspire/ident/peptide.rb
- lib/mspire/ident/peptide/db.rb
- lib/mspire/ident/peptide/db/creator.rb
- lib/mspire/ident/peptide/db/io.rb
- lib/mspire/ident/peptide_hit.rb
- lib/mspire/ident/peptide_hit/qvalue.rb
- lib/mspire/ident/pepxml.rb
- lib/mspire/ident/pepxml/modifications.rb
- lib/mspire/ident/pepxml/msms_pipeline_analysis.rb
- lib/mspire/ident/pepxml/msms_run_summary.rb
- lib/mspire/ident/pepxml/parameters.rb
- lib/mspire/ident/pepxml/sample_enzyme.rb
- lib/mspire/ident/pepxml/search_database.rb
- lib/mspire/ident/pepxml/search_hit.rb
- lib/mspire/ident/pepxml/search_hit/modification_info.rb
- lib/mspire/ident/pepxml/search_result.rb
- lib/mspire/ident/pepxml/search_summary.rb
- lib/mspire/ident/pepxml/spectrum_query.rb
- lib/mspire/ident/protein.rb
- lib/mspire/ident/protein_group.rb
- lib/mspire/ident/search.rb
- lib/mspire/imzml/writer.rb
- lib/mspire/imzml/writer/commandline.rb
- lib/mspire/isotope.rb
- lib/mspire/isotope/aa.rb
- lib/mspire/isotope/distribution.rb
- lib/mspire/isotope/neese.rb
- lib/mspire/isotope/nist.rb
- lib/mspire/isotope/nist/isotope_info.yml
- lib/mspire/isotope/nist/updater.rb
- lib/mspire/mascot.rb
- lib/mspire/mass.rb
- lib/mspire/mass/aa.rb
- lib/mspire/mass/all.rb
- lib/mspire/mass/common.rb
- lib/mspire/mass/element.rb
- lib/mspire/mass/subatomic.rb
- lib/mspire/mass/util.rb
- lib/mspire/molecular_formula.rb
- lib/mspire/mzid/modification.rb
- lib/mspire/mzid/search_modification.rb
- lib/mspire/mzml.rb
- lib/mspire/mzml/activation.rb
- lib/mspire/mzml/chromatogram.rb
- lib/mspire/mzml/chromatogram_list.rb
- lib/mspire/mzml/component.rb
- lib/mspire/mzml/contact.rb
- lib/mspire/mzml/cv.rb
- lib/mspire/mzml/data_array.rb
- lib/mspire/mzml/data_array_container_like.rb
- lib/mspire/mzml/data_processing.rb
- lib/mspire/mzml/file_content.rb
- lib/mspire/mzml/file_description.rb
- lib/mspire/mzml/index.rb
- lib/mspire/mzml/index_list.rb
- lib/mspire/mzml/instrument_configuration.rb
- lib/mspire/mzml/io_index.rb
- lib/mspire/mzml/io_indexable_list.rb
- lib/mspire/mzml/isolation_window.rb
- lib/mspire/mzml/list.rb
- lib/mspire/mzml/parser.rb
- lib/mspire/mzml/plms1.rb
- lib/mspire/mzml/precursor.rb
- lib/mspire/mzml/processing_method.rb
- lib/mspire/mzml/product.rb
- lib/mspire/mzml/reader.rb
- lib/mspire/mzml/referenceable_param_group.rb
- lib/mspire/mzml/run.rb
- lib/mspire/mzml/sample.rb
- lib/mspire/mzml/scan.rb
- lib/mspire/mzml/scan_list.rb
- lib/mspire/mzml/scan_settings.rb
- lib/mspire/mzml/scan_window.rb
- lib/mspire/mzml/selected_ion.rb
- lib/mspire/mzml/software.rb
- lib/mspire/mzml/source_file.rb
- lib/mspire/mzml/spectrum.rb
- lib/mspire/mzml/spectrum_list.rb
- lib/mspire/obo.rb
- lib/mspire/paramable.rb
- lib/mspire/peak.rb
- lib/mspire/peaklist.rb
- lib/mspire/plms1.rb
- lib/mspire/quant/cmdline.rb
- lib/mspire/quant/protein_group_comparison.rb
- lib/mspire/quant/qspec.rb
- lib/mspire/quant/qspec/protein_group_comparison.rb
- lib/mspire/quant/spectral_counts.rb
- lib/mspire/spectrum.rb
- lib/mspire/spectrum/centroid.rb
- lib/mspire/spectrum_like.rb
- lib/mspire/tagged_peak.rb
- lib/mspire/user_param.rb
- lib/mspire/version.rb
- lib/obo/ims.rb
- lib/obo/ms.rb
- lib/obo/ontology.rb
- lib/obo/unit.rb
- lib/openany.rb
- lib/write_file_or_string.rb
- mspire.gemspec
- obo/ims.obo
- obo/mod.obo
- obo/ms.obo
- obo/unit.obo
- schema/peptide_hit_qvalues.pqh.tsv
- script/accession_quantifier.rb
- script/download_uniprotkb_db.rb
- script/fasta_to_peptide_centric_db.rb
- script/mascot_dat_to_peptide_hit_qvalues.rb
- script/mass_correct.rb
- script/minimal_protein_set.rb
- script/mzml_read_binary.rb
- script/mzml_to_mgf.rb
- script/peptide_hit_qvalues_to_spectral_counts_table.rb
- script/quant_compare_direct_injections.rb
- spec/cv/param_spec.rb
- spec/mspire/bin_spec.rb
- spec/mspire/cv/obo_spec.rb
- spec/mspire/cv/param_spec.rb
- spec/mspire/cv/paramable_spec.rb
- spec/mspire/digester_spec.rb
- spec/mspire/error_rate/qvalue_spec.rb
- spec/mspire/fasta_spec.rb
- spec/mspire/ident/peptide/db/creator_spec.rb
- spec/mspire/ident/peptide/db/io_spec.rb
- spec/mspire/ident/peptide/db_spec.rb
- spec/mspire/ident/pepxml/sample_enzyme_spec.rb
- spec/mspire/ident/pepxml/search_hit/modification_info_spec.rb
- spec/mspire/ident/pepxml_spec.rb
- spec/mspire/ident/protein_group_spec.rb
- spec/mspire/imzml/writer_spec.rb
- spec/mspire/isotope/aa_spec.rb
- spec/mspire/isotope/distribution_spec.rb
- spec/mspire/isotope/nist_spec.rb
- spec/mspire/isotope_spec.rb
- spec/mspire/mass/aa_spec.rb
- spec/mspire/mass/all_spec.rb
- spec/mspire/mass/common_spec.rb
- spec/mspire/mass/element_spec.rb
- spec/mspire/mass/subatomic_spec.rb
- spec/mspire/mass_spec.rb
- spec/mspire/molecular_formula_spec.rb
- spec/mspire/mzml/cv_spec.rb
- spec/mspire/mzml/data_array_spec.rb
- spec/mspire/mzml/file_content_spec.rb
- spec/mspire/mzml/index_list_spec.rb
- spec/mspire/mzml/plms1_spec.rb
- spec/mspire/mzml/referenceable_param_group_spec.rb
- spec/mspire/mzml/source_file_spec.rb
- spec/mspire/mzml/spectrum_list_spec.rb
- spec/mspire/mzml/spectrum_spec.rb
- spec/mspire/mzml_spec.rb
- spec/mspire/peaklist_spec.rb
- spec/mspire/plms1_spec.rb
- spec/mspire/quant/qspec_spec.rb
- spec/mspire/readme_spec.rb
- spec/mspire/spectrum_spec.rb
- spec/mspire/user_param_spec.rb
- spec/mspire_spec.rb
- spec/obo_spec.rb
- spec/spec_helper.rb
- spec/spec_utilities.rb
- spec/testfiles/continuous_binary.tmp.ibd
- spec/testfiles/mspire/ident/peptide/db/uni_11_sp_tr.PEPTIDE_CENTRIC.yml
- spec/testfiles/mspire/ident/peptide/db/uni_11_sp_tr.fasta
- spec/testfiles/mspire/ident/peptide/db/uni_11_sp_tr.msd_clvg2.min_aaseq4.yml
- spec/testfiles/mspire/imzml/1_BB7_SIM_478.5.CHECK.ibd
- spec/testfiles/mspire/imzml/1_BB7_SIM_478.5.CHECK.imzML
- spec/testfiles/mspire/imzml/continuous_binary.CHECK.ibd
- spec/testfiles/mspire/imzml/processed_binary.CHECK.ibd
- spec/testfiles/mspire/mzml/1_BB7_SIM_478.5.mzML
- spec/testfiles/mspire/mzml/j24z.idx_comp.3.NORMALIZED.CHECK.mzML
- spec/testfiles/mspire/mzml/j24z.idx_comp.3.ROUNDTRIP.CHECK.mzML
- spec/testfiles/mspire/mzml/j24z.idx_comp.3.mzML
- spec/testfiles/mspire/mzml/mspire_simulated.MSn.CHECK.mzML
- spec/testfiles/mspire/mzml/openms.noidx_nocomp.12.mzML
- spec/testfiles/mspire/quant/kill_extra_tabs.rb
- spec/testfiles/mspire/quant/max_quant_output.provenance.txt
- spec/testfiles/mspire/quant/max_quant_output.txt
- spec/testfiles/mspire/quant/pdcd5_final.killedextratabs.tsv
- spec/testfiles/mspire/quant/pdcd5_final.killedextratabs.tsv_qspecgp
- spec/testfiles/mspire/quant/pdcd5_final.killedextratabs.tsv_qspecgp.csv
- spec/testfiles/mspire/quant/pdcd5_final.txt
- spec/testfiles/mspire/quant/pdcd5_final.txt_qspecgp
- spec/testfiles/mspire/quant/pdcd5_lfq_qspec.CSV.csv
- spec/testfiles/mspire/quant/pdcd5_lfq_qspec.csv
- spec/testfiles/mspire/quant/pdcd5_lfq_qspec.oneprot.csv
- spec/testfiles/mspire/quant/pdcd5_lfq_qspec.oneprot.tsv
- spec/testfiles/mspire/quant/pdcd5_lfq_qspec.oneprot.tsv_qspecgp
- spec/testfiles/mspire/quant/pdcd5_lfq_qspec.oneprot.tsv_qspecgp.csv
- spec/testfiles/mspire/quant/pdcd5_lfq_qspec.txt
- spec/testfiles/mspire/quant/pdcd5_lfq_tabdel.txt
- spec/testfiles/mspire/quant/pdcd5_lfq_tabdel.txt_qspecgp
- spec/testfiles/mspire/quant/remove_rest_of_proteins.rb
- spec/testfiles/mspire/quant/unlog_transform.rb
- spec/testfiles/plms1/output.key
- spec/testfiles/processed_binary.tmp.ibd
homepage: http://github.com/princelab/mspire
licenses:
- MIT
metadata: {}
post_install_message: 
rdoc_options: []
require_paths:
- lib
required_ruby_version: !ruby/object:Gem::Requirement
  requirements:
  - - ">="
    - !ruby/object:Gem::Version
      version: '0'
required_rubygems_version: !ruby/object:Gem::Requirement
  requirements:
  - - ">="
    - !ruby/object:Gem::Version
      version: '0'
requirements: []
rubyforge_project: 
rubygems_version: 2.2.0
signing_key: 
specification_version: 4
summary: mass spectrometry proteomics, lipidomics, and tools
test_files:
- spec/cv/param_spec.rb
- spec/mspire/bin_spec.rb
- spec/mspire/cv/obo_spec.rb
- spec/mspire/cv/param_spec.rb
- spec/mspire/cv/paramable_spec.rb
- spec/mspire/digester_spec.rb
- spec/mspire/error_rate/qvalue_spec.rb
- spec/mspire/fasta_spec.rb
- spec/mspire/ident/peptide/db/creator_spec.rb
- spec/mspire/ident/peptide/db/io_spec.rb
- spec/mspire/ident/peptide/db_spec.rb
- spec/mspire/ident/pepxml/sample_enzyme_spec.rb
- spec/mspire/ident/pepxml/search_hit/modification_info_spec.rb
- spec/mspire/ident/pepxml_spec.rb
- spec/mspire/ident/protein_group_spec.rb
- spec/mspire/imzml/writer_spec.rb
- spec/mspire/isotope/aa_spec.rb
- spec/mspire/isotope/distribution_spec.rb
- spec/mspire/isotope/nist_spec.rb
- spec/mspire/isotope_spec.rb
- spec/mspire/mass/aa_spec.rb
- spec/mspire/mass/all_spec.rb
- spec/mspire/mass/common_spec.rb
- spec/mspire/mass/element_spec.rb
- spec/mspire/mass/subatomic_spec.rb
- spec/mspire/mass_spec.rb
- spec/mspire/molecular_formula_spec.rb
- spec/mspire/mzml/cv_spec.rb
- spec/mspire/mzml/data_array_spec.rb
- spec/mspire/mzml/file_content_spec.rb
- spec/mspire/mzml/index_list_spec.rb
- spec/mspire/mzml/plms1_spec.rb
- spec/mspire/mzml/referenceable_param_group_spec.rb
- spec/mspire/mzml/source_file_spec.rb
- spec/mspire/mzml/spectrum_list_spec.rb
- spec/mspire/mzml/spectrum_spec.rb
- spec/mspire/mzml_spec.rb
- spec/mspire/peaklist_spec.rb
- spec/mspire/plms1_spec.rb
- spec/mspire/quant/qspec_spec.rb
- spec/mspire/readme_spec.rb
- spec/mspire/spectrum_spec.rb
- spec/mspire/user_param_spec.rb
- spec/mspire_spec.rb
- spec/obo_spec.rb
- spec/spec_helper.rb
- spec/spec_utilities.rb
- spec/testfiles/continuous_binary.tmp.ibd
- spec/testfiles/mspire/ident/peptide/db/uni_11_sp_tr.PEPTIDE_CENTRIC.yml
- spec/testfiles/mspire/ident/peptide/db/uni_11_sp_tr.fasta
- spec/testfiles/mspire/ident/peptide/db/uni_11_sp_tr.msd_clvg2.min_aaseq4.yml
- spec/testfiles/mspire/imzml/1_BB7_SIM_478.5.CHECK.ibd
- spec/testfiles/mspire/imzml/1_BB7_SIM_478.5.CHECK.imzML
- spec/testfiles/mspire/imzml/continuous_binary.CHECK.ibd
- spec/testfiles/mspire/imzml/processed_binary.CHECK.ibd
- spec/testfiles/mspire/mzml/1_BB7_SIM_478.5.mzML
- spec/testfiles/mspire/mzml/j24z.idx_comp.3.NORMALIZED.CHECK.mzML
- spec/testfiles/mspire/mzml/j24z.idx_comp.3.ROUNDTRIP.CHECK.mzML
- spec/testfiles/mspire/mzml/j24z.idx_comp.3.mzML
- spec/testfiles/mspire/mzml/mspire_simulated.MSn.CHECK.mzML
- spec/testfiles/mspire/mzml/openms.noidx_nocomp.12.mzML
- spec/testfiles/mspire/quant/kill_extra_tabs.rb
- spec/testfiles/mspire/quant/max_quant_output.provenance.txt
- spec/testfiles/mspire/quant/max_quant_output.txt
- spec/testfiles/mspire/quant/pdcd5_final.killedextratabs.tsv
- spec/testfiles/mspire/quant/pdcd5_final.killedextratabs.tsv_qspecgp
- spec/testfiles/mspire/quant/pdcd5_final.killedextratabs.tsv_qspecgp.csv
- spec/testfiles/mspire/quant/pdcd5_final.txt
- spec/testfiles/mspire/quant/pdcd5_final.txt_qspecgp
- spec/testfiles/mspire/quant/pdcd5_lfq_qspec.CSV.csv
- spec/testfiles/mspire/quant/pdcd5_lfq_qspec.csv
- spec/testfiles/mspire/quant/pdcd5_lfq_qspec.oneprot.csv
- spec/testfiles/mspire/quant/pdcd5_lfq_qspec.oneprot.tsv
- spec/testfiles/mspire/quant/pdcd5_lfq_qspec.oneprot.tsv_qspecgp
- spec/testfiles/mspire/quant/pdcd5_lfq_qspec.oneprot.tsv_qspecgp.csv
- spec/testfiles/mspire/quant/pdcd5_lfq_qspec.txt
- spec/testfiles/mspire/quant/pdcd5_lfq_tabdel.txt
- spec/testfiles/mspire/quant/pdcd5_lfq_tabdel.txt_qspecgp
- spec/testfiles/mspire/quant/remove_rest_of_proteins.rb
- spec/testfiles/mspire/quant/unlog_transform.rb
- spec/testfiles/plms1/output.key
- spec/testfiles/processed_binary.tmp.ibd