bio-octopus 0.1.0 → 0.1.1

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Files changed (6) hide show
  1. data/README.rdoc +9 -0
  2. data/VERSION +1 -1
  3. data/bin/biooctopus +21 -6
  4. data/bin/biooctopus.rb +21 -6
  5. data/bio-octopus.gemspec +2 -2
  6. metadata +4 -4
data/README.rdoc CHANGED
@@ -2,6 +2,15 @@
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  A bioruby plugin for running and parsing octopus, available from http://octopus.cbr.su.se/ Currently, the plugin is not Ruby 1.9 (only 1.8) compatible, because of the dependency on the rio gem.
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+ To run it as a script, a fasta file of sequences to predict, and a database formatted in legacy blast database format needs to be specified:
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+
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+ $ /usr/local/rvm/gems/ruby-1.8.7-p334/gems/bio-octopus-0.1.0/bin/biooctopus my.fasta /blastdb/UniProt2011_04/uniprot_sprot.fasta
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+
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+ Output are topology predictions, including signal peptide and transmembrane domain predictions. If that is not the best format for you, look at the script file and modify it - it is just a front-end. Also required are:
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+ * a working install of SPOCTOPUS
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+ * NCBI legacy blast
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+ Binaries for these must be accessible in the PATH.
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+
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  == Contributing to bio-octopus
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  * Check out the latest master to make sure the feature hasn't been implemented or the bug hasn't been fixed yet
data/VERSION CHANGED
@@ -1 +1 @@
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- 0.1.0
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+ 0.1.1
data/bin/biooctopus CHANGED
@@ -1,7 +1,7 @@
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  #!/usr/bin/env ruby
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  #
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  # BioRuby bio-octopus Plugin
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- # Version 0.0.1
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+ # Version 0.1.1
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  # Author:: Ben J Woodcroft
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  # Copyright:: 2011
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  # License:: The Ruby License
@@ -21,12 +21,12 @@ if $0 == __FILE__
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  ].flatten
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  end
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  o.parse!
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-
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+
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  unless ARGV.length == 2
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- puts o.help
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- exit
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+ puts o.help
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+ exit
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  end
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-
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+
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  fasta_path = ARGV[0]
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  blastdb_path = ARGV[1]
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@@ -36,6 +36,21 @@ if $0 == __FILE__
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  result = runner.calculate(seq.seq, blastdb_path)
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  name = seq.definition
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+ # Output singal peptide if it has one
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+ if result.signal?
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+ puts [
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+ name,
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+ 'Signal peptide',
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+ result.signal_peptide.start,
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+ result.signal_peptide.stop
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+ ].join("\t")
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+ else
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+ puts [
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+ name,
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+ 'No signal peptide found'
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+ ].join("\t")
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+ end
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+
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  if result.has_domain?
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  # At least one TMD found. Output each on a separate line
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  result.transmembrane_domains.each do |tmd|
@@ -50,7 +65,7 @@ if $0 == __FILE__
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  else
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  puts [
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  name,
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- 'No Transmembrane Domain Found'
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+ 'No transmembrane domain found'
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  ].join("\t")
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  end
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  end
data/bin/biooctopus.rb CHANGED
@@ -1,7 +1,7 @@
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  #!/usr/bin/env ruby
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  #
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  # BioRuby bio-octopus Plugin
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- # Version 0.0.1
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+ # Version 0.1.1
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  # Author:: Ben J Woodcroft
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  # Copyright:: 2011
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  # License:: The Ruby License
@@ -21,12 +21,12 @@ if $0 == __FILE__
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  ].flatten
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  end
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  o.parse!
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-
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+
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  unless ARGV.length == 2
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- puts o.help
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- exit
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+ puts o.help
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+ exit
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  end
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-
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+
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  fasta_path = ARGV[0]
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  blastdb_path = ARGV[1]
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@@ -36,6 +36,21 @@ if $0 == __FILE__
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  result = runner.calculate(seq.seq, blastdb_path)
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  name = seq.definition
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+ # Output singal peptide if it has one
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+ if result.signal?
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+ puts [
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+ name,
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+ 'Signal peptide',
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+ result.signal_peptide.start,
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+ result.signal_peptide.stop
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+ ].join("\t")
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+ else
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+ puts [
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+ name,
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+ 'No signal peptide found'
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+ ].join("\t")
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+ end
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+
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  if result.has_domain?
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  # At least one TMD found. Output each on a separate line
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  result.transmembrane_domains.each do |tmd|
@@ -50,7 +65,7 @@ if $0 == __FILE__
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  else
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  puts [
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  name,
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- 'No Transmembrane Domain Found'
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+ 'No transmembrane domain found'
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  ].join("\t")
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  end
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  end
data/bio-octopus.gemspec CHANGED
@@ -5,11 +5,11 @@
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  Gem::Specification.new do |s|
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  s.name = %q{bio-octopus}
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- s.version = "0.1.0"
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+ s.version = "0.1.1"
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  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
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  s.authors = ["Ben J Woodcroft"]
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- s.date = %q{2011-04-17}
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+ s.date = %q{2011-05-02}
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  s.description = %q{Running and parsing of the protein transmembrane domain predictor octopus}
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  s.email = %q{gmail.com after donttrustben}
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  s.executables = ["biooctopus.rb", "biooctopus"]
metadata CHANGED
@@ -1,13 +1,13 @@
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  --- !ruby/object:Gem::Specification
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  name: bio-octopus
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  version: !ruby/object:Gem::Version
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- hash: 27
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+ hash: 25
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  prerelease:
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  segments:
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  - 0
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  - 1
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- - 0
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- version: 0.1.0
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+ - 1
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+ version: 0.1.1
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  platform: ruby
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  authors:
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  - Ben J Woodcroft
@@ -15,7 +15,7 @@ autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2011-04-17 00:00:00 +10:00
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+ date: 2011-05-02 00:00:00 +10:00
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  default_executable:
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  dependencies:
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  - !ruby/object:Gem::Dependency