protk 1.3.1.pre3 → 1.4.0

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Files changed (44) hide show
  1. checksums.yaml +4 -4
  2. data/README.md +21 -19
  3. data/bin/add_retention_times.rb +1 -1
  4. data/bin/interprophet.rb +16 -5
  5. data/bin/make_decoy.rb +1 -1
  6. data/bin/manage_db.rb +1 -1
  7. data/bin/mascot_search.rb +2 -2
  8. data/bin/mascot_to_pepxml.rb +1 -1
  9. data/bin/msgfplus_search.rb +26 -9
  10. data/bin/omssa_search.rb +1 -1
  11. data/bin/peptide_prophet.rb +57 -20
  12. data/bin/pepxml_to_table.rb +15 -2
  13. data/bin/protein_prophet.rb +41 -1
  14. data/bin/protk_setup.rb +2 -2
  15. data/bin/protxml_to_gff.rb +50 -42
  16. data/bin/protxml_to_psql.rb +1 -1
  17. data/bin/protxml_to_table.rb +16 -3
  18. data/bin/repair_run_summary.rb +1 -1
  19. data/bin/sixframe.rb +2 -2
  20. data/bin/swissprot_to_table.rb +1 -1
  21. data/bin/tandem_search.rb +1 -1
  22. data/bin/tandem_to_pepxml.rb +1 -1
  23. data/lib/protk/constants.rb +2 -1
  24. data/lib/protk/convert_util.rb +1 -1
  25. data/lib/protk/data/tandem-style.css +349 -0
  26. data/lib/protk/data/tandem-style.xsl +264 -0
  27. data/lib/protk/data/tandem_gpm_defaults.xml +3 -3
  28. data/lib/protk/data/tandem_isb_kscore_defaults.xml +2 -0
  29. data/lib/protk/data/tandem_isb_native_defaults.xml +3 -0
  30. data/lib/protk/data/tandem_params.xml +0 -8
  31. data/lib/protk/fastadb.rb +1 -1
  32. data/lib/protk/galaxy_stager.rb +14 -3
  33. data/lib/protk/galaxy_util.rb +39 -31
  34. data/lib/protk/gffdb.rb +6 -1
  35. data/lib/protk/manage_db_rakefile.rake +1 -1
  36. data/lib/protk/manage_db_tool.rb +1 -1
  37. data/lib/protk/pepxml.rb +159 -7
  38. data/lib/protk/plasmodb.rb +1 -1
  39. data/lib/protk/prophet_tool.rb +20 -52
  40. data/lib/protk/setup_rakefile.rake +18 -11
  41. data/lib/protk/tandem_search_tool.rb +20 -7
  42. data/lib/protk/tool.rb +1 -1
  43. data/lib/protk/uniprot_mapper.rb +1 -1
  44. metadata +10 -14
data/lib/protk/tool.rb CHANGED
@@ -203,7 +203,7 @@ class Tool
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  db_path=Pathname.new(@options.database).expand_path.to_s
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  db_name=Pathname.new(@options.database).basename.to_s
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  else
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- db_path=Constants.new.current_database_for_name @options.database
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+ db_path=Constants.instance.current_database_for_name @options.database
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  db_name=@options.database
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  end
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  FastaDatabase.new(db_name,db_path)
data/lib/protk/uniprot_mapper.rb CHANGED
@@ -8,7 +8,7 @@ require 'protk/constants'
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  class UniprotMapper
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  def initialize
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- @genv = Constants.new
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+ @genv = Constants.instance
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  end
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  def map(from_id_type,from_ids,output_id)
metadata CHANGED
@@ -1,14 +1,14 @@
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  --- !ruby/object:Gem::Specification
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  name: protk
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  version: !ruby/object:Gem::Version
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- version: 1.3.1.pre3
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+ version: 1.4.0
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  platform: ruby
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  authors:
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  - Ira Cooke
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  autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2014-10-06 00:00:00.000000000 Z
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+ date: 2015-05-01 00:00:00.000000000 Z
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  dependencies:
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  - !ruby/object:Gem::Dependency
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  name: open4
@@ -153,25 +153,19 @@ dependencies:
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  - !ruby/object:Gem::Version
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  version: '0'
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  - !ruby/object:Gem::Dependency
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- name: debugger
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+ name: byebug
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  requirement: !ruby/object:Gem::Requirement
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  requirements:
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  - - ~>
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  - !ruby/object:Gem::Version
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- version: '1.6'
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- - - '>='
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- - !ruby/object:Gem::Version
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- version: 1.6.0
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+ version: '3.5'
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  type: :development
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  prerelease: false
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  version_requirements: !ruby/object:Gem::Requirement
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  requirements:
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  - - ~>
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  - !ruby/object:Gem::Version
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- version: '1.6'
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- - - '>='
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- - !ruby/object:Gem::Version
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- version: 1.6.0
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+ version: '3.5'
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  - !ruby/object:Gem::Dependency
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  name: sqlite3
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  requirement: !ruby/object:Gem::Requirement
@@ -186,7 +180,7 @@ dependencies:
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  - - ~>
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  - !ruby/object:Gem::Version
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  version: '0'
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- description: A bunch of tools for proteomics
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+ description: Commandline tools for proteomics
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  email: iracooke@gmail.com
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  executables:
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  - protk_setup.rb
@@ -260,6 +254,8 @@ files:
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  - lib/protk/data/predefined_db.sphuman.yaml
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  - lib/protk/data/predefined_db.swissprot_annotation.yaml
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  - lib/protk/data/predefined_db.swissprot_fasta_annotation.yaml
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+ - lib/protk/data/tandem-style.css
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+ - lib/protk/data/tandem-style.xsl
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  - lib/protk/data/tandem_gpm_defaults.xml
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  - lib/protk/data/tandem_isb_kscore_defaults.xml
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  - lib/protk/data/tandem_isb_native_defaults.xml
@@ -310,9 +306,9 @@ required_ruby_version: !ruby/object:Gem::Requirement
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  version: '0'
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  required_rubygems_version: !ruby/object:Gem::Requirement
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  requirements:
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- - - '>'
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+ - - '>='
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  - !ruby/object:Gem::Version
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- version: 1.3.1
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+ version: '0'
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  requirements: []
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  rubyforge_project:
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  rubygems_version: 2.2.1