lib/genevalidator/blast.rb in genevalidator-1.6.2 vs lib/genevalidator/blast.rb in genevalidator-1.6.3

@@ -2,12 +2,12 @@
 require 'bio-blastxmlparser'
 require 'forwardable'
 
 require 'genevalidator/exceptions'
 require 'genevalidator/hsp'
-require 'genevalidator/sequences'
 require 'genevalidator/output'
+require 'genevalidator/query'
 
 module GeneValidator
   # Contains methods that run BLAST and methods that analyse sequences
   class BlastUtils
     class << self
@@ -34,11 +34,11 @@
 
         blastcmd = "#{blast_type} -db '#{db}' -evalue #{EVALUE} -outfmt 5" \
                    " #{threads}"
 
         cmd = "echo \"#{query}\" | #{blastcmd}"
-        `#{cmd} 2>/dev/null`
+        `#{cmd} >/dev/null 2>&1`
       end
 
       ##
       # Runs BLAST on an input file
       # Params:
@@ -52,26 +52,31 @@
       def run_blast_on_input_file(input_file = opt[:input_fasta_file],
                                   db = opt[:db], seq_type = config[:type],
                                   num_threads = opt[:num_threads])
         return if opt[:blast_xml_file] || opt[:blast_tabular_file]
 
-        $stderr.puts 'Running BLAST'
+        $stderr.puts 'Running BLAST. This may take a while.'
         opt[:blast_xml_file] = input_file + '.blast_xml'
 
         blast_type = (seq_type == :protein) ? 'blastp' : 'blastx'
         # -num_threads is not supported on remote databases
         threads = (opt[:db] !~ /remote/) ? "-num_threads #{num_threads}" : ''
 
         blastcmd = "#{blast_type} -query '#{input_file}'" \
                    " -out '#{opt[:blast_xml_file]}' -db #{db} " \
                    " -evalue #{EVALUE} -outfmt 5 #{threads}"
 
-        `#{blastcmd}`
+        `#{blastcmd} >/dev/null 2>&1`
         return unless File.zero?(opt[:blast_xml_file])
-        $stderr.puts 'Blast failed to run on the input file. Please ensure that the'
-        $stderr.puts 'BLAST database exists and try again'
-        exit 1
+        $stderr.puts 'Blast failed to run on the input file.'
+        if opt[:db] !~ /remote/
+          $stderr.puts 'Please ensure that the BLAST database exists and try'
+          $stderr.puts 'again.'
+        else
+          $stderr.puts 'You are using BLAST with a remote database. Please'
+          $stderr.puts 'ensure that you have internet access and try again.'
+        end
       end
 
       ##
       # Parses the next query from the blast xml output query
       # Params:
@@ -84,11 +89,11 @@
         iter = iterator.next
 
         # parse blast the xml output and get the hits
         # hits obtained are proteins! (we use only blastp and blastx)
         iter.each do |hit|
-          seq = Sequence.new
+          seq = Query.new
 
           seq.length_protein = hit.len.to_i
           seq.type           = :protein
           seq.identifier     = hit.hit_id
           seq.definition     = hit.hit_def
@@ -124,11 +129,12 @@
             if guess_sequence_type(current_hsp.query_alignment) != :protein
               fail SequenceTypeError
             end
             current_hsp.align_len = hsp.align_len.to_i
             current_hsp.identity  = hsp.identity.to_i
-            current_hsp.pidentity = (100 * hsp.identity / (hsp.align_len + 0.0)).round(2)
+            current_hsp.pidentity = (100 * hsp.identity / hsp.align_len.to_f)
+              .round(2)
 
             hsps.push(current_hsp)
           end
 
           seq.hsp_list = hsps
@@ -156,13 +162,14 @@
       # nil, :nucleotide or :protein
       def type_of_sequences(fasta_format_string)
         # the first sequence does not need to have a fasta definition line
         sequences = fasta_format_string.split(/^>.*$/).delete_if(&:empty?)
         # get all sequence types
-        sequence_types = sequences.collect { |seq| guess_sequence_type(seq) }.uniq.compact
+        sequence_types = sequences.collect { |seq| guess_sequence_type(seq) }
+                         .uniq.compact
 
         return nil if sequence_types.empty?
-        return sequence_types.first if sequence_types.length == 1
+        sequence_types.first if sequence_types.length == 1
       end
 
       ##
       # Strips all non-letter characters. guestimates sequence based on that.
       # If less than 10 useable characters... returns nil