protk 1.2.6.pre1 → 1.2.6.pre2
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +7 -0
- data/README.md +22 -27
- data/bin/blastxml_to_table.rb +50 -3
- data/bin/make_decoy.rb +30 -2
- data/bin/mascot_search.rb +46 -27
- data/bin/msgfplus_search.rb +7 -4
- data/bin/peptide_prophet.rb +9 -0
- data/bin/protxml_to_gff.rb +122 -66
- data/bin/protxml_to_table.rb +26 -3
- data/bin/tandem_search.rb +1 -1
- data/lib/protk/constants.rb +19 -19
- data/lib/protk/data/default_config.yml +0 -7
- data/lib/protk/search_tool.rb +7 -0
- metadata +118 -90
- data/bin/mascot2xml.rb +0 -87
- data/ext/protk/simplealign/simplealign.c +0 -17
- data/lib/protk/data/pepxml_mascot_template.xml +0 -29
- data/lib/protk/data/predefined_db.trembl_annotation.yaml +0 -20
data/bin/protxml_to_table.rb
CHANGED
@@ -19,6 +19,11 @@ include LibXML
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tool=Tool.new([:explicit_output])
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tool.option_parser.banner = "Convert a protXML file to a tab delimited table.\n\nUsage: protxml_to_table.rb [options] file1.protXML"
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+
tool.options.groups=false
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+
tool.option_parser.on("--groups","Print output by groups rather than for each protein") do
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tool.options.groups=true
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end
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+
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# tool.options.proteinid_regex=".*?\|.*?\|(.*)"
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# tool.option_parser.on( '--regex rexpr', 'Regex' ) do |regex|
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# tool.options.proteinid_regex=regex
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@@ -58,8 +63,10 @@ column_headers=[
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"num_peptides","confidence"
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]
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-
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+
groups_column_headers=["group_number","group_probability","members"]
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+
output_fh.write "#{column_headers.join("\t")}\n" unless tool.groups
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+
output_fh.write "#{groups_column_headers.join("\t")}\n" if tool.groups
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protein_groups=protxml_doc.find("//#{protxml_ns_prefix}protein_group", protxml_ns)
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@@ -67,6 +74,8 @@ protein_groups.each do |protein_group|
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proteins=protein_group.find("./#{protxml_ns_prefix}protein", protxml_ns)
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+
group_members=[]
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+
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proteins.each do |protein|
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indis_proteins=protein.find("./#{protxml_ns_prefix}indistinguishable_protein", protxml_ns)
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@@ -78,6 +87,8 @@ protein_groups.each do |protein_group|
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protein_id=protein.attributes['protein_name'].match(/.*?\|.*?\|(.*)/)[1]
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end
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+
group_members<<protein.attributes['protein_name']
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+
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column_values=[]
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column_values << protein_group.attributes['group_number']
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@@ -91,9 +102,21 @@ protein_groups.each do |protein_group|
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column_values << protein.attributes['unique_stripped_peptides']
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column_values << protein.attributes['total_number_peptides']
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column_values << protein.attributes['confidence']
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-
output_fh.write(column_values.join("\t"))
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-
output_fh.write("\n")
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+
unless tool.groups
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output_fh.write(column_values.join("\t"))
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+
output_fh.write("\n")
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end
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end
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+
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+
group_column_values=[protein_group.attributes['group_number']]
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+
group_column_values<<protein_group.attributes['probability']
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+
group_column_values<<group_members.join(" ")
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+
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if tool.groups
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+
output_fh.write(group_column_values.join("\t"))
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output_fh.write("\n")
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+
end
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+
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end
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data/bin/tandem_search.rb
CHANGED
@@ -22,7 +22,7 @@ genv=Constants.new
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#
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search_tool=SearchTool.new([:background,:glyco,:database,:explicit_output,:over_write,
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:enzyme,:modifications,:mass_tolerance_units,:mass_tolerance,:strict_monoisotopic_mass,
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-
:missed_cleavages,:carbamidomethyl,:methionine_oxidation
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+
:missed_cleavages,:cleavage_semi,:carbamidomethyl,:methionine_oxidation
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])
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search_tool.jobid_prefix="x"
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search_tool.option_parser.banner = "Run an X!Tandem msms search on a set of mzML input files.\n\nUsage: tandem_search.rb [options] file1.mzML file2.mzML ..."
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data/lib/protk/constants.rb
CHANGED
@@ -133,7 +133,7 @@ class Constants
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end
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def msgfplusjar
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-
return
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+
return %x[which MSGFPlus.jar]
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end
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def pwiz_root
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@@ -236,7 +236,7 @@ class Constants
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@protk_dir=ENV['PROTK_INSTALL_DIR']
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end
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-
# Protk Defaults
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+
# Load Protk Defaults
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#
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default_config_yml = YAML.load_file "#{File.dirname(__FILE__)}/data/default_config.yml"
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throw "Unable to read the config file at #{File.dirname(__FILE__)}/data/default_config.yml" unless default_config_yml!=nil
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@@ -251,31 +251,31 @@ class Constants
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@env=default_config_yml
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end
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-
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+
protk_tool_dirs=["tpp","omssa","openms","msgfplus","blast","pwiz","tandem"]
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+
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# Construct the PATH variable by prepending our preferred paths
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#
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-
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+
protk_paths=[]
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-
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-
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+
# Add PATHs if PROTK_XXX_ROOT is defined
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+
#
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+
protk_tool_dirs.each do |tooldir|
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+
env_value = ENV["PROTK_#{tooldir.upcase}_ROOT"]
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if ( env_value!=nil)
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-
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-
if env_value=="FROMPATH"
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-
bin_path=Pathname.new(%x[which #{binaryname}].chomp)
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-
if bin_path.exist?
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-
env_value=bin_path.realpath.dirname.to_s
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-
else
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-
env_value=""
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-
end
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-
end
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-
p "Using #{r} root #{env_value}"
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-
@env["#{r}_root"]=env_value
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+
protk_paths<<env_value
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end
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+
protk_paths<<"#{@protk_dir}/tools/#{tooldir}"
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end
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+
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+
original_path=ENV['PATH']
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+
protk_paths<<original_path
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+
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+
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+
ENV['PATH']=protk_paths.join(":")
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+
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throw "No data found in config file" unless @env!=nil
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@info_level=default_config_yml['message_level']
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-
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-
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end
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@@ -12,11 +12,4 @@ uniprot_sprot_annotation_database: swissprot_annotation
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uniprot_trembl_annotation_database: trembl_annotation
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galaxy_root: galaxy
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default_mascot_server: www.matrixscience.com
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-
tpp_root: tools/tpp
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-
omssa_root: tools/omssa
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-
openms_root: tools/openms
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-
msgfplus_root: tools/msgfplus
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-
blast_root: tools/blast
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-
pwiz_root: tools/pwiz
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-
tandem_root: tools/tandem
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log_file: Logs/protk.log
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data/lib/protk/search_tool.rb
CHANGED
@@ -100,6 +100,13 @@ class SearchTool < Tool
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end
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end
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+
if ( option_support.include? :cleavage_semi )
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@options.cleavage_semi=true
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@option_parser.on( '--no-cleavage-semi', 'Dont allow up to 1 non tryptic terminus on peptides' ) do
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@options.cleavage_semi=false
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end
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+
end
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+
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if ( option_support.include? :respect_precursor_charges )
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@options.respect_precursor_charges=false
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@option_parser.on( '-q', '--respect-charges','Dont respect charges in the input file. Instead impute them by trying various options') do
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metadata
CHANGED
@@ -1,8 +1,7 @@
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1
1
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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: 1.2.6.
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-
prerelease: 6
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+
version: 1.2.6.pre2
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platform: ruby
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authors:
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- Ira Cooke
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@@ -14,151 +13,186 @@ dependencies:
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- !ruby/object:Gem::Dependency
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name: ftools
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requirement: !ruby/object:Gem::Requirement
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none: false
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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: '0.0'
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- - '>='
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- !ruby/object:Gem::Version
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version: 0.0.0
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type: :runtime
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
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none: false
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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: '0.0'
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+
- - '>='
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- !ruby/object:Gem::Version
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version: 0.0.0
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- !ruby/object:Gem::Dependency
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name: open4
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requirement: !ruby/object:Gem::Requirement
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none: false
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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'
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+
- - '>='
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- !ruby/object:Gem::Version
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version: 1.3.0
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type: :runtime
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
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-
none: false
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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'
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+
- - '>='
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- !ruby/object:Gem::Version
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version: 1.3.0
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- !ruby/object:Gem::Dependency
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name: bio
|
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requirement: !ruby/object:Gem::Requirement
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-
none: false
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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: '1.4'
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+
- - '>='
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- !ruby/object:Gem::Version
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version: 1.4.3
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type: :runtime
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
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-
none: false
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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: '1.4'
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+
- - '>='
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- !ruby/object:Gem::Version
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version: 1.4.3
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- !ruby/object:Gem::Dependency
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name: rest-client
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requirement: !ruby/object:Gem::Requirement
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-
none: false
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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: 1.6.7
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+
- - '>='
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- !ruby/object:Gem::Version
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version: 1.6.7
|
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type: :runtime
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
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-
none: false
|
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requirements:
|
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-
- -
|
87
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+
- - ~>
|
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+
- !ruby/object:Gem::Version
|
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+
version: 1.6.7
|
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+
- - '>='
|
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- !ruby/object:Gem::Version
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version: 1.6.7
|
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- !ruby/object:Gem::Dependency
|
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name: net-ftp-list
|
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requirement: !ruby/object:Gem::Requirement
|
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-
none: false
|
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requirements:
|
83
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-
- -
|
97
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+
- - ~>
|
98
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+
- !ruby/object:Gem::Version
|
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+
version: 3.2.5
|
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+
- - '>='
|
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- !ruby/object:Gem::Version
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version: 3.2.5
|
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type: :runtime
|
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prerelease: false
|
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version_requirements: !ruby/object:Gem::Requirement
|
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-
none: false
|
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requirements:
|
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|
-
- -
|
107
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+
- - ~>
|
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+
- !ruby/object:Gem::Version
|
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+
version: 3.2.5
|
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+
- - '>='
|
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- !ruby/object:Gem::Version
|
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version: 3.2.5
|
94
113
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- !ruby/object:Gem::Dependency
|
95
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|
name: spreadsheet
|
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requirement: !ruby/object:Gem::Requirement
|
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-
none: false
|
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requirements:
|
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-
- -
|
117
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+
- - ~>
|
118
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+
- !ruby/object:Gem::Version
|
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+
version: 0.7.4
|
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+
- - '>='
|
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- !ruby/object:Gem::Version
|
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version: 0.7.4
|
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type: :runtime
|
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prerelease: false
|
104
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version_requirements: !ruby/object:Gem::Requirement
|
105
|
-
none: false
|
106
126
|
requirements:
|
107
|
-
- -
|
127
|
+
- - ~>
|
128
|
+
- !ruby/object:Gem::Version
|
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+
version: 0.7.4
|
130
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+
- - '>='
|
108
131
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- !ruby/object:Gem::Version
|
109
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version: 0.7.4
|
110
133
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- !ruby/object:Gem::Dependency
|
111
134
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name: libxml-ruby
|
112
135
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requirement: !ruby/object:Gem::Requirement
|
113
|
-
none: false
|
114
136
|
requirements:
|
115
|
-
- -
|
137
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+
- - ~>
|
116
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- !ruby/object:Gem::Version
|
117
|
-
version: 2.
|
139
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+
version: '2.7'
|
140
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+
- - '>='
|
141
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+
- !ruby/object:Gem::Version
|
142
|
+
version: 2.7.0
|
118
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|
type: :runtime
|
119
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|
prerelease: false
|
120
145
|
version_requirements: !ruby/object:Gem::Requirement
|
121
|
-
none: false
|
122
146
|
requirements:
|
123
|
-
- -
|
147
|
+
- - ~>
|
124
148
|
- !ruby/object:Gem::Version
|
125
|
-
version: 2.
|
149
|
+
version: '2.7'
|
150
|
+
- - '>='
|
151
|
+
- !ruby/object:Gem::Version
|
152
|
+
version: 2.7.0
|
126
153
|
- !ruby/object:Gem::Dependency
|
127
154
|
name: mascot-dat
|
128
155
|
requirement: !ruby/object:Gem::Requirement
|
129
|
-
none: false
|
130
156
|
requirements:
|
131
|
-
- -
|
157
|
+
- - ~>
|
158
|
+
- !ruby/object:Gem::Version
|
159
|
+
version: 0.3.1
|
160
|
+
- - '>='
|
132
161
|
- !ruby/object:Gem::Version
|
133
162
|
version: 0.3.1
|
134
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|
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|
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|
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