ms-error_rate 0.0.9 → 0.0.10
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- data/.autotest +14 -0
- data/.gitmodules +9 -0
- data/History +16 -0
- data/LICENSE +2 -0
- data/Rakefile +52 -0
- data/VERSION +1 -1
- data/lib/ms/error_rate/decoy.rb +27 -0
- data/lib/ms/error_rate/qvalue/mascot/percolator.rb +93 -0
- data/lib/ms/error_rate/qvalue/mascot.rb +68 -0
- data/lib/ms/error_rate/qvalue/pepxml.rb +52 -0
- data/lib/ms/error_rate/qvalue.rb +93 -0
- data/lib/ms/error_rate/sbv/peptide_based.rb +30 -0
- data/lib/ms/error_rate/sbv/protein_based.rb +39 -0
- data/lib/ms/error_rate/sbv.rb +111 -0
- data/lib/ms/error_rate.rb +9 -0
- data/lib/ms/ident.rb +125 -0
- data/lib/support/sort_by_attributes.rb +51 -0
- data/lib/transmembrane/phobius.rb +136 -0
- data/lib/transmembrane/toppred.rb +368 -0
- data/lib/transmembrane.rb +157 -0
- data/schema/peptide_hit_qvalues.pqh.tsv +5 -0
- data/script/expert_addition.rb +26 -0
- data/script/expert_list.rb +53 -0
- data/script/fasta_ipi_to_ipi_decoy.rb +23 -0
- data/script/minimal_protein_set.rb +366 -0
- data/script/unique_seq_stats.rb +72 -0
- metadata +66 -14
metadata
CHANGED
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@@ -5,11 +5,11 @@ version: !ruby/object:Gem::Version
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segments:
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- 0
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version: 0.0.
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- 10
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version: 0.0.10
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platform: ruby
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authors:
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- John
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- John Prince
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autorequire:
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bindir: bin
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cert_chain: []
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@@ -33,7 +33,7 @@ dependencies:
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type: :runtime
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version_requirements: *id001
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- !ruby/object:Gem::Dependency
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name: ms-
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name: ms-ident
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prerelease: false
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requirement: &id002 !ruby/object:Gem::Requirement
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none: false
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@@ -42,9 +42,9 @@ dependencies:
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segments:
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version: 0.
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- 0
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- 20
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version: 0.0.20
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type: :runtime
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version_requirements: *id002
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- !ruby/object:Gem::Dependency
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@@ -60,6 +60,34 @@ dependencies:
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version: "0"
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type: :development
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version_requirements: *id003
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- !ruby/object:Gem::Dependency
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name: jeweler
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prerelease: false
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requirement: &id004 !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ~>
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- !ruby/object:Gem::Version
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segments:
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- 1
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- 5
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- 2
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version: 1.5.2
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type: :development
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version_requirements: *id004
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- !ruby/object:Gem::Dependency
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name: rcov
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prerelease: false
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requirement: &id005 !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ">="
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- !ruby/object:Gem::Version
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segments:
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- 0
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version: "0"
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type: :development
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version_requirements: *id005
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description: aids for creating and calculating error rates using target-decoy searches and sample validation.
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email: jtprince@gmail.com
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executables:
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@@ -78,12 +106,13 @@ extra_rdoc_files:
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- LICENSE
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- README.rdoc
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files:
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- .autotest
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- .gitmodules
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- History
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- LICENSE
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- README.rdoc
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- spec/spec_helper.rb
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- Rakefile
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- VERSION
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- bin/error_rate
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- bin/fasta_to_nuclear.rb
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- bin/fasta_to_peptide_centric_db.rb
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@@ -93,10 +122,33 @@ files:
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- bin/mascot_pepxml_to_peptide_hit_qvalues.rb
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- bin/phobius_to_nontransmembrane.rb
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- bin/qvalues.rb
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- lib/ms/error_rate.rb
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- lib/ms/error_rate/decoy.rb
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- lib/ms/error_rate/qvalue.rb
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- lib/ms/error_rate/qvalue/mascot.rb
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- lib/ms/error_rate/qvalue/mascot/percolator.rb
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- lib/ms/error_rate/qvalue/pepxml.rb
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- lib/ms/error_rate/sbv.rb
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- lib/ms/error_rate/sbv/peptide_based.rb
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- lib/ms/error_rate/sbv/protein_based.rb
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- lib/ms/ident.rb
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- lib/support/sort_by_attributes.rb
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136
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- lib/transmembrane.rb
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137
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- lib/transmembrane/phobius.rb
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138
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- lib/transmembrane/toppred.rb
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139
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- schema/peptide_hit_qvalues.pqh.tsv
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140
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- script/expert_addition.rb
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141
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- script/expert_list.rb
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142
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- script/fasta_ipi_to_ipi_decoy.rb
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143
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- script/minimal_protein_set.rb
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144
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- script/unique_seq_stats.rb
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145
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- spec/ms/error_rate/qvalue_spec.rb
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- spec/ms/error_rate_spec.rb
|
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147
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- spec/spec_helper.rb
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96
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has_rdoc: true
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homepage: http://
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licenses:
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-
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149
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homepage: http://github.com/jtprince/ms-error_rate
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licenses:
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151
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+
- MIT
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100
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post_install_message:
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101
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rdoc_options: []
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102
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