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Contents
require "fasta_reader.rb"
######################################
# Author:: Almudena Bocinos Rioboo
# Extract ramdom sequences until "num_seqs"
# Inherit:: FastaReader
######################################
class ExtractSamples < FastaReader
attr_accessor :num_seqs
def initialize(file_name)
@num_seqs = 0
super(file_name)
end
# override begin processing
def on_begin_process()
$LOG.info " Begin Extract Samples"
@fich = File.open("results/Sample.txt",'w')
@max = 1000
end
# override processing sequence
def on_process_sequence(seq_name,seq_fasta)
ra_seq = Kernel.rand
if ((@num_seqs < @max) and (ra_seq>0.5)) #if cond is successful then, choose a part from this sequence
#calculate the part from the sequence
width = (Kernel.rand * 50 ) + 300
ra_part1 = Kernel.rand * (seq_fasta.length-width)
ra_part2 = ra_part1 + width
sub_seq_fasta = seq_fasta.slice(ra_part1,ra_part2)
@fich.puts "#{seq_name} "
@fich.puts "#{sub_seq_fasta} "
@num_seqs += 1
end
end
#override end processing
def on_end_process()
$LOG.info "All Samples have been extracted"
@fich.close
end
end
Version data entries
28 entries across 28 versions & 1 rubygems