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

@@ -24,11 +24,10 @@
 
         assert_validations_arg
         check_num_threads
 
         export_bin_dirs unless @opt[:bin].nil?
-
         Blast.validate(opt) unless @opt[:test]
         assert_mafft_installation
       end
 
       # Return `true` if the given command exists and is executable.
@@ -51,11 +50,12 @@
         @opt[:num_threads] = Integer(@opt[:num_threads])
         unless @opt[:num_threads] > 0
           $stderr.puts 'Number of threads can not be lower than 0'
         end
         return unless @opt[:num_threads] > 256
-        $stderr.puts "Number of threads set at #{@opt[:num_threads]} is unusually high."
+        $stderr.puts "Number of threads set at #{@opt[:num_threads]} is" \
+                     ' unusually high.'
       end
 
       def assert_BLAST_output_files
         return unless @opt[:blast_xml_file] || @opt[:blast_tabular_file]
         if @opt[:blast_xml_file]
@@ -67,12 +67,12 @@
       end
 
       def assert_output_dir_does_not_exist
         output_dir = "#{@opt[:input_fasta_file]}.html"
         return unless File.exist?(output_dir)
-        $stderr.puts "The output directory already exists for this fasta file.\n"
-        $stderr.puts "Please remove the following directory: #{output_dir}\n"
+        $stderr.puts 'The output directory already exists for this fasta file.'
+        $stderr.puts "\nPlease remove the following directory: #{output_dir}\n"
         $stderr.puts "You can run the following command to remove the folder.\n"
         $stderr.puts "\n   $ rm -r #{output_dir} \n"
         exit 1
       end
 
@@ -100,28 +100,31 @@
 
       def assert_input_sequence
         fasta_content = IO.binread(@opt[:input_fasta_file])
         type = BlastUtils.type_of_sequences(fasta_content)
         return if type == :nucleotide || type == :protein
-        $stderr.puts '*** Error: The input files does not contain just protein or'
-        $stderr.puts '    nucleotide data. Please correct this and try again.'
+        $stderr.puts '*** Error: The input files does not contain just protein'
+        $stderr.puts '    or nucleotide data.'
+        $stderr.puts '    Please correct this and try again.'
         exit 1
       end
 
       def export_bin_dirs
         @opt[:bin].each do |bin|
-          if File.directory?(bin)
+          bin = File.expand_path(bin)
+          if File.exist?(bin) && File.directory?(bin)
             add_to_path(bin)
           else
             $stderr.puts '*** The following bin directory does not exist:'
             $stderr.puts "    #{bin}"
           end
         end
       end
 
       ## Checks if dir is in $PATH and if not, it adds the dir to the $PATH.
       def add_to_path(bin_dir)
+        return unless bin_dir
         return if ENV['PATH'].split(':').include?(bin_dir)
         ENV['PATH'] = "#{bin_dir}:#{ENV['PATH']}"
       end
 
       def assert_mafft_installation
@@ -155,15 +158,15 @@
           assert_blast_compatible
         end
 
         def warn_if_remote_database(db)
           return if db !~ /remote/
-          $stderr.puts # a blank line
+          $stderr.puts # a blank line
           $stderr.puts 'Warning: BLAST will be carried out on remote servers.'
           $stderr.puts 'This may take quite a bit of time.'
           $stderr.puts 'You may want to install a local BLAST database for' \
                        ' faster analyses.'
-          $stderr.puts # a blank line
+          $stderr.puts # a blank line
         end
 
         def assert_local_blast_database_exists(db)
           return if system("blastdbcmd -db #{db} -info > /dev/null 2>&1")
           $stderr.puts '*** No BLAST database found at the provided path.'