class OneBlast
Public Class Methods
new(database, blast_type = 'blastp')
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# File lib/seqtrimnext/classes/one_blast.rb, line 5 def initialize(database, blast_type = 'blastp') @blast_type = blast_type @database = database @c=0 end
Public Instance Methods
close()
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# File lib/seqtrimnext/classes/one_blast.rb, line 35 def close end
do_blast(seq_fasta)
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# File lib/seqtrimnext/classes/one_blast.rb, line 13 def do_blast(seq_fasta) @f = File.new('one_blast_aux.fasta','w+') @f.puts ">SEQNAME_"+@c.to_s @f.puts seq_fasta @c = @c+1 @f.close cmd = '~blast/programs/x86_64/bin/blastall -p '+@blast_type+' -d '+@database + ' -i one_blast_aux.fasta -o one_blast_aux.out' #puts cmd system(cmd) res ='' File.open('one_blast_aux.out').each_line { |line| res = line } end