SilkSlider 0.1.0 → 0.2.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: f46fdc69dee531983bef5fa6c99b460693f4d74f
-  data.tar.gz: 17e84f801770f8e6acede7f750f1514d12fc6ae5
+  metadata.gz: ad393f3f24c8137ec1817bb55295068dd5ce4af6
+  data.tar.gz: d3376592a5646b87db935532e8de336403c24f63
 SHA512:
-  metadata.gz: 347c0cb9b39eb0ffa6bc04aaf1fa3198789e4b9cec1f6a90adc6da36da57fb1401d3123a0e734c543ae6705d785daf5d881e1ed33a0bbfd4a919f3858c7ebc91
-  data.tar.gz: ec2b31727a8ec2bc4fc30c13ba67544c94c26db42364bbb610c8dc7e19748036d69b2432af071e00b195f67268a53057e3ecd7da3340db777d20010a2a839451
+  metadata.gz: f9a00a8bb7641df0c92e7c85956266d6c003f591bb6897e7168b46e67e79a85b1ff4f013436cfa3e991d5473a501ff087dcce1f014f7372713352beee0666492
+  data.tar.gz: 350b0eadbb521d99ae82868c9127c51df7b0bab7a805256144d8ee78ee447c4e88e05441407af63e7937d566c2c13588ebb0e87d7bc1ef2d7c0ed71b2719db78

data/README.md

@@ -21,7 +21,8 @@ To run the program:
 ```sh
 silk_slider my.fasta
 ```
-The program outputs a 
+The program outputs a FASTA file of all silk-like proteins.
+
 To see the help:
 ```sh
 silk_slider -h

data/VERSION

@@ -1 +1 @@
-0.1.0
+0.2.0

data/bin/silk_slider

@@ -35,6 +35,9 @@ o = OptionParser.new do |opts|
   opts.on("--min-glycines NUM", Integer, "Number of glycines in a window for the protein to be considered silk-like, as an absolute number (not percentage) [default: #{options[:min_glycines] }]") do |arg|
     options[:min_glycines] = arg
   end
+  opts.on("--signalp-binary PATH", "Path to signalp binary to use [default: use 'signalp' on $PATH }]") do |arg|
+    options[:signalp_binary] = arg
+  end
   opts.separator "\nVerbosity:\n\n"
   opts.on("-q", "--quiet", "Run quietly, set logging to ERROR level [default INFO]") {options[:log_level] = 'error'}
   opts.on("--logger filename",String,"Log to file [default #{options[:logger]}]") { |name| options[:logger] = name}
@@ -52,12 +55,21 @@ Bio::Log::CLI.logger(options[:logger]); Bio::Log::CLI.trace(options[:log_level])
 signalp_runner = Bio::SignalP::Wrapper.new
 tmhmm_runner = Bio::TMHMM::TmHmmWrapper.new
 
+example_result = nil
+num_predicted = 0
+num_considered = 0
+
 Bio::FlatFile.open(Bio::FastaFormat, ARGF).each do |seq|
-  signalp_result = signalp_runner.calculate(seq.seq)
+  signalp_result = signalp_runner.calculate(seq.seq, :binary_path => options[:signalp_binary])
   if signalp_result.nil?
     $stderr.puts "Unexpected empty sequence detected, ignoring: #{seq.definition}"
     next
   end
+  if example_result.nil?
+    example_result = signalp_result
+    log.info "Using SignalP version: #{example_result.class}" if log.info?
+  end
+  num_considered += 1
 
   log.debug "Sequence #{seq.definition} predicted by SignalP? #{signalp_result.prediction}" if log.debug?
   if signalp_result.prediction
@@ -75,7 +87,10 @@ Bio::FlatFile.open(Bio::FastaFormat, ARGF).each do |seq|
         # We have a winner. Output.
         puts ">#{seq.definition}"
         puts seq.seq
+        num_predicted += 1
       end
     end
   end
 end
+
+log.info "Predicted #{num_predicted} out of #{num_considered} as silk-like" if log.info?

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: SilkSlider
 version: !ruby/object:Gem::Version
-  version: 0.1.0
+  version: 0.2.0
 platform: ruby
 authors:
 - Carmel McDougall
@@ -10,7 +10,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-07-02 00:00:00.000000000 Z
+date: 2014-07-13 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio-signalp