EXT_OPTION = 'e'
EXTRACT_LINKERS_OPTION = 'l'
LOG_SUFFIX = ".mse_log"
+ LINKERS_SUFFIX = ".linkers"
FASTA_SUFFIX = ".fasta"
FASTA_WITH_NORMALIZED_IDS_SUFFIX = ".ni.fasta"
NORMALIZED_IDS_MAP_SUFFIX = ".nim"
new_msa_domains = Msa.new
new_msa_domains_extended = Msa.new
per_species_counter = 0
-
+ linkers = ""
+
puts basename
-
+
File.open( input_file ) do | file |
while line = file.gets
line.strip!
new_msa_normalized_ids.add_sequence( Sequence.new( normalized_id, seq.get_sequence_as_string ) )
if mod_line
- puts mod_line
+ linkers << mod_line + Constants::LINE_DELIMITER
end
end # !Util.is_string_empty?( line ) && !(line =~ /\s*#/ )
end # while line = file.gets
rescue Exception => e
Util.fatal_error( PRG_NAME, "error: " + e.to_s )
end
+
+ if extract_linkers
+ begin
+ f = File.open( out_dir + Constants::FILE_SEPARATOR + basename + LINKERS_SUFFIX , 'a' )
+ f.print( linkers )
+ f.close
+ rescue Exception => e
+ Util.fatal_error( PRG_NAME, "error: " + e.to_s )
+ end
+ end
+
end