Contents

require 'scbi_fasta'


def load_isoform_hash(file)
	isoform_hash = {}
	if File.exists?(file)
		fasta = FastaQualFile.new(file)
		fasta.each do |name, seq, desc|
			name =~ /(\w+\|(\w+)\-\d+\|)/
			if isoform_hash[$2].nil?
				isoform_hash[$2] = ">#{$1}#{desc}\n#{seq}"
			else
				isoform_hash[$2] += "\n>#{$1}#{desc}\n#{seq}"
			end
		end
		fasta.close
	end
	return isoform_hash
end

def do_makeblastdb(seqs, output, dbtype)
	cmd="makeblastdb -in - -out #{output} -title #{File.basename(output)} -dbtype #{dbtype} -parse_seqids"
	IO.popen(cmd,'w+') {|makedb|
		makedb.sync = TRUE
		makedb.write(seqs)
		makedb.close_write
		puts makedb.readlines
		makedb.close_read
	}
end

Version data entries

4 entries across 4 versions & 1 rubygems

Version	Path
full_lengther_next-0.6.1	lib/full_lengther_next/classes/handle_db.rb
full_lengther_next-0.6.0	lib/full_lengther_next/classes/handle_db.rb
full_lengther_next-0.5.7	lib/full_lengther_next/classes/handle_db.rb
full_lengther_next-0.5.6	lib/full_lengther_next/classes/handle_db.rb