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Merge pull request #35 from unipept/migrated/pr-35/feature/add-tests
Add tests and improve code style
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,26 @@ | ||
| AllCops: | ||
| Include: | ||
| - | ||
| Exclude: | ||
| - 'unipept.gemspec' | ||
| - 'vendor/**/*' | ||
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| Style/ClassAndModuleChildren: | ||
| EnforcedStyle: compact | ||
| Enabled: false | ||
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| # disable for now | ||
| Style/ClassVars: | ||
| Enabled: false | ||
| Style/Documentation: | ||
| Enabled: false | ||
| Style/RescueModifier: | ||
| Enabled: false | ||
| Metrics/AbcSize: | ||
| Enabled: false | ||
| Metrics/ClassLength: | ||
| Enabled: false | ||
| Metrics/LineLength: | ||
| Enabled: false | ||
| Metrics/MethodLength: | ||
| Enabled: false |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,7 @@ | ||
| language: ruby | ||
| rvm: | ||
| - 2.2.2 | ||
| - 2.1.6 | ||
| - 2.0.0 | ||
| - 1.9.3 | ||
| - jruby-19mode |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,17 +1,15 @@ | ||
| source "http://rubygems.org" | ||
| source 'http://rubygems.org' | ||
| # Add dependencies required to use your gem here. | ||
| # Example: | ||
| # gem "activesupport", ">= 2.3.5" | ||
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| gem "cri", "~> 2.7" | ||
| gem "typhoeus", "~> 0.6" | ||
| gem 'cri', '~> 2.7' | ||
| gem 'typhoeus', '~> 0.6' | ||
|
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| # Add dependencies to develop your gem here. | ||
| # Include everything needed to run rake, tests, features, etc. | ||
| group :development do | ||
| gem "shoulda", "~> 3.5" | ||
| gem "rdoc", "~> 3.12" | ||
| gem "bundler", "~> 1.0" | ||
| gem "jeweler", "~> 2.0" | ||
| gem "simplecov", "~> 0.8" | ||
| gem 'rake' | ||
| gem 'minitest' | ||
| gem 'rubocop' | ||
| gem 'jeweler' | ||
| gem 'coveralls', require: false | ||
| end |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,49 +1,7 @@ | ||
| #!/usr/bin/env ruby | ||
| require 'cri' | ||
| require_relative '../lib/commands' | ||
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| Signal.trap('PIPE', 'EXIT') | ||
| Signal.trap('INT', 'EXIT') | ||
| root_cmd = Cri::Command.new_basic_root.modify do | ||
| name 'peptfilter' | ||
| summary 'Filter peptides based on specific criteria.' | ||
| usage 'peptfilter [options]' | ||
| description <<-EOS | ||
| The peptfilter command filters a list of peptides according to specific criteria. The command expects a list of peptides that are passed | ||
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| - as separate command line arguments | ||
| - in one or more text files that are passed as an argument to the -i option | ||
| - to standard input | ||
| The command will give priority to the first way peptides are passed, in the order as listed above. Text files and standard input should have one peptide per line. FASTA headers are preserved in the output, so that peptides remain bundled. | ||
| EOS | ||
| # flag :u, :unique, "filter duplicate peptides." | ||
| required nil, :minlen, 'only retain tryptic peptides that have at least min (default: 5) amino acids.' | ||
| required nil, :maxlen, 'only retain tryptic peptides that have at most max (default: 50) amino acids.' | ||
| required :l, :lacks, 'only retain tryptic peptides that lack all amino acids from the string of residues.' | ||
| required :c, :contains, 'only retain tryptic peptides that contain all amino acids from the string of residues.' | ||
| run do |opts, _args, _cmd| | ||
| minlen = opts.fetch(:minlen, '5').to_i | ||
| maxlen = opts.fetch(:maxlen, '50').to_i | ||
| lacks = opts.fetch(:lacks, '').chars.to_a | ||
| contains = opts.fetch(:contains, '').chars.to_a | ||
| $stdin.each_line do |pept| | ||
| # FASTA headers | ||
| if pept.start_with? '>' | ||
| puts pept | ||
| next | ||
| end | ||
| pept = pept.chomp | ||
| length_ok = pept.length >= minlen && pept.length <= maxlen | ||
| lacks_ok = (pept.chars.to_a & lacks).size == 0 | ||
| contains_ok = (pept.chars.to_a & contains).size == contains.size | ||
|
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| if length_ok && lacks_ok && contains_ok | ||
| puts pept | ||
| end | ||
| end | ||
| end | ||
| end | ||
|
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| root_cmd.run(ARGV) | ||
| Unipept::Commands::Peptfilter.run(ARGV) |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,52 +1,7 @@ | ||
| #!/usr/bin/env ruby | ||
| require 'cri' | ||
| require_relative '../lib/commands' | ||
|
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| Signal.trap("PIPE", "EXIT") | ||
| Signal.trap("INT", "EXIT") | ||
| root_cmd = Cri::Command.new_basic_root.modify do | ||
| name 'prot2pept' | ||
| summary 'Split protein sequences into peptides.' | ||
| usage 'prot2pept [options]' | ||
| description <<-EOS | ||
| The prot2pept command splits each protein sequence into a list of peptides according to a given cleavage-pattern. The command expects a list of protein sequences that are passed | ||
| Signal.trap('PIPE', 'EXIT') | ||
| Signal.trap('INT', 'EXIT') | ||
|
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||
| - as separate command line arguments | ||
| - in one or more text files that are passed as an argument to the -i option | ||
| - to standard input | ||
| The command will give priority to the first way protein sequences are passed, in the order as listed above. Text files and standard input should have either one protein sequence per line or contain a FASTA formatted list of protein sequences. FASTA headers are preserved in the output, so that peptides can be bundled per protein sequence. | ||
| EOS | ||
| required :p, :pattern, 'specify cleavage-pattern (regex) as the pattern after which the next peptide will be cleaved (default: ([KR])([^P]) for tryptic peptides).' | ||
| run do |opts, args, cmd| | ||
| pattern = opts.fetch(:pattern, "([KR])([^P])") | ||
| # decide if we have FASTA input | ||
| fasta_header = $stdin.gets | ||
| if fasta_header.start_with? '>' | ||
| # fasta input, need to join lines | ||
| while !$stdin.eof? | ||
| prot = "" | ||
| # Sometimes you just got to accept this weird and ugly code | ||
| until $stdin.eof? || (line = gets).start_with?('>') | ||
| prot += line.chomp | ||
| end | ||
| puts fasta_header | ||
| puts prot.gsub(/#{pattern}/,"\\1\n\\2").gsub(/#{pattern}/, "\\1\n\\2").split("\n").reject(&:empty?) | ||
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| fasta_header = line | ||
| end | ||
| else | ||
| # handle our already read line | ||
| puts fasta_header.gsub(/#{pattern}/,"\\1\n\\2").gsub(/#{pattern}/, "\\1\n\\2").split("\n").reject(&:empty?) | ||
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| # we no longer have to join lines as input is now more sane | ||
| $stdin.each_line do |prot| | ||
| puts prot.gsub(/#{pattern}/,"\\1\n\\2").gsub(/#{pattern}/, "\\1\n\\2").split("\n").reject(&:empty?) | ||
| end | ||
| end | ||
| end | ||
| end | ||
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| root_cmd.run(ARGV) | ||
| Unipept::Commands::Prot2pept.run(ARGV) |
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