def initialize()
@file_to_msa = Hash.new
+ @seqs = 0
end
def run()
puts basename
File.open( input_file ) do | file |
+ species_counter = 1
while line = file.gets
line.strip!
if !Util.is_string_empty?( line ) && !(line =~ /\s*#/ )
print_counts( per_species_counter, log, Constants::LINE_DELIMITER )
per_species_counter = 0
end
- puts " " + current_species + " [" + my_readlink + "]"
- log << current_species + " [" + my_readlink + "]" + Constants::LINE_DELIMITER
+ puts " " + species_counter.to_s + ":" + current_species + " [" + my_readlink + "]"
+ log << species_counter.to_s + ": " + current_species + " [" + my_readlink + "]" + Constants::LINE_DELIMITER
+ species_counter += 1
end
puts " " + seq_name
log << " " + seq_name + Constants::LINE_DELIMITER
rescue Exception => e
Util.fatal_error( PRG_NAME, "error: " + e.to_s )
end
- if @file_to_msa.size < 400 && msa.get_number_of_seqs < 40000
+ if @seqs <= 100000000
@file_to_msa[ input ] = msa
+ @seqs += msa.get_number_of_seqs
+ puts " total seqs in memory: " + @seqs.to_s
end
msa
end