neurohmmer 0.1.1 → 0.1.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: 0c48aaea036d17b839b62d751313590224dce84c
+  metadata.gz: db09d40ef755f21f24d634b0ccbc99b931451284
+  data.tar.gz: 0c5206d2a6e780321087cbb08b372eedd360a432
 SHA512:
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+  data.tar.gz: 8a910895b19c9cc131a4ec477875076a356b8f205a49734552b12d0bc866e9ea6285c3500abfa67bbcb1cb0520891bbc653e0af2b7905f510e4aabd81c71ef13

data/bin/neurohmmer

@@ -1,5 +1,6 @@
 #!/usr/bin/env ruby
 require 'optparse'
+require 'English'
 
 require 'neurohmmer'
 require 'neurohmmer/version'
@@ -36,7 +37,7 @@ BANNER
     opt[:signalp_path] = s
   end
 
-  opts.on('-b', '--hmmer_bin_path path',
+  opts.on('-H', '--hmmer_bin_path path',
           'The full path to hmmer binaries directory') do |h|
     opt[:hmmer_path] = h
   end
@@ -70,7 +71,7 @@ begin
     exit 1
   end
 rescue OptionParser::ParseError
-  $stderr.print 'Error: ' + $ERROR_INFO.to_s + '\n'
+  $stderr.print 'Error: ' + $ERROR_INFO.to_s + "\n"
   exit 1
 end
 

data/lib/neurohmmer.rb

@@ -19,7 +19,8 @@ module Neurohmmer
         raw_alignments: File.expand_path('../../data/raw_data/alignments',
                                          __FILE__),
         hmm_output: File.join(@opt[:temp_dir], 'input.hmm_search.out'),
-        html_output: "#{@opt[:input_file]}.neurohmmer.html"
+        html_output: "#{@opt[:input_file]}.neurohmmer.html",
+        fasta_output: "#{@opt[:input_file]}.neurohmmer.fa"
       }
       init_input
     end
@@ -27,6 +28,7 @@ module Neurohmmer
     def run
       Hmmer.search
       hmm_analysis = Hmmer.analyse_output
+      Output.to_fasta(hmm_analysis)
       Output.to_html(hmm_analysis)
       remove_temp_dir
     end

data/lib/neurohmmer/arg_validators.rb

@@ -11,7 +11,7 @@ module Neurohmmer
         assert_input_file_probably_fasta(opt[:input_file])
         opt[:type] = assert_input_sequence(opt[:input_file])
         export_bin_dirs(opt[:hmmer_bin]) if opt[:hmmer_bin]
-        # TODO: Assert hmm & mafft binaries
+        # TODO: Assert mafft binaries
         opt
       end
 
@@ -69,9 +69,9 @@ module Neurohmmer
       end
 
       def export_bin_dirs(hmmer_bin)
-        bin = File.expand_path(bin)
+        bin = File.expand_path(hmmer_bin)
         if File.exist?(bin) && File.directory?(bin)
-          add_to_path(bin) 
+          add_to_path(bin)
         else
           $stderr.puts '*** The following bin directory does not exist:'
           $stderr.puts "    #{bin}"

data/lib/neurohmmer/hmmer.rb

@@ -13,7 +13,8 @@ module Neurohmmer
         Dir.foreach(conf[:hmm_dir]) do |h|
           hmm_file = File.join(conf[:hmm_dir], h)
           next if hmm_file !~ /hmm$/
-          hmm_search(opt[:input_file], hmm_file, conf[:hmm_output])
+          hmm_search(opt[:input_file], hmm_file, conf[:hmm_output],
+                     opt[:num_threads])
         end
       end
 
@@ -36,7 +37,7 @@ module Neurohmmer
                                      "#{file.gsub(/fa(sta)?$/, '')}.aligned")
           hmm_model_file = File.join(conf[:hmm_dir],
                                      "#{file.gsub(/fa(sta)?$/, '')}.hmm")
-          mafft(np_fasta_file, aligned_file, conf[:num_threads])
+          mafft(np_fasta_file, aligned_file, opt[:num_threads])
           hmm_build(aligned_file, hmm_model_file)
         end
       end
@@ -63,8 +64,9 @@ module Neurohmmer
         `hmmbuild '#{hmm_model_file}' '#{aligned_file}'`
       end
 
-      def hmm_search(input_file, hmm_file, hmm_output)
-        `hmmsearch '#{hmm_file}' '#{input_file}' >> '#{hmm_output}'`
+      def hmm_search(input_file, hmm_file, hmm_output, num_threads)
+        `hmmsearch --cpu #{num_threads} '#{hmm_file}' '#{input_file}' >> \
+        '#{hmm_output}'`
       end
     end
   end

data/lib/neurohmmer/output.rb

@@ -11,6 +11,20 @@ module Neurohmmer
       extend Forwardable
       def_delegators Neurohmmer, :opt, :conf
 
+      def to_fasta(hmm_results)
+        File.open(conf[:fasta_output], 'w') do |file|
+          hmm_results.each do |query, hits|
+            next if hits.length == 0
+            file.puts # a blank line
+            file.puts '# ' + query
+            hits.each do |hit|
+              file.puts '>' + hit[:id]
+              file.puts hit[:seq]
+            end
+          end
+        end
+      end
+
       def to_html(hmm_results)
         @html_results = format_seqs_for_html(hmm_results)
         template_path = File.expand_path('../../../template/contents.slim',
@@ -64,12 +78,12 @@ module Neurohmmer
           s = s1.gsub(/<span class=hsp>/, '</span><span class=sp_hsp>') +
               seq[sp_cut_off..-1]
           return s.insert(0, '<span class=sp>')
-                  .insert(sp_cut_off + 41, '</span><span class=hsp>')
+            .insert(sp_cut_off + 41, '</span><span class=hsp>')
         elsif s1 =~ /</
-          s = s1.gsub(/<.+$/, '</span><span class=sp_hsp>') +
-              seq[sp_cut_off..-1].gsub(/^\w+?>/,'')
+          s = s1.gsub(/<.*?$/, '</span><span class=sp_hsp>') +
+              seq[sp_cut_off..-1].gsub(/^.*?>/, '')
           return s.insert(0, '<span class=sp>')
-                  .insert(sp_cut_off + 41, '</span><span class=hsp>')
+            .insert(sp_cut_off + 41, '</span><span class=hsp>')
         else
           return seq.insert(0, '<span class=sp>').insert(sp_cut_off + 15,
                                                          '</span>')

data/lib/neurohmmer/version.rb

@@ -1,4 +1,4 @@
 # Top level module / namespace.
 module Neurohmmer
-  VERSION = '0.1.1'
+  VERSION = '0.1.2'
 end

data/template/contents.slim

@@ -53,5 +53,5 @@ html lang="en"
         a href="http://www.sbcs.qmul.ac.uk" target="_blank" QMUL
         br
         | This page was created by 
-        a href="https://github.com/wurmlab/NpSearch" target="_blank"  NpSearch 
+        a href="https://github.com/wurmlab/neurohmmer" target="_blank"  NeuroHMMer 
         | v#{Neurohmmer::VERSION}

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: neurohmmer
 version: !ruby/object:Gem::Version
-  version: 0.1.1
+  version: 0.1.2
 platform: ruby
 authors:
 - Ismail Moghul
@@ -10,7 +10,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-11-18 00:00:00.000000000 Z
+date: 2015-11-23 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler