COPYRIGHT = "2008-2010 Christian M Zmasek"
CONTACT = "phylosoft@gmail.com"
WWW = "www.phylosoft.org"
COPYRIGHT = "2008-2010 Christian M Zmasek"
CONTACT = "phylosoft@gmail.com"
WWW = "www.phylosoft.org"
allowed_opts.push( REM_RED_OPTION )
allowed_opts.push( KEEP_MATCHING_SEQUENCES_OPTION )
allowed_opts.push( REMOVE_MATCHING_SEQUENCES_OPTION )
allowed_opts.push( REM_RED_OPTION )
allowed_opts.push( KEEP_MATCHING_SEQUENCES_OPTION )
allowed_opts.push( REMOVE_MATCHING_SEQUENCES_OPTION )
Util.fatal_error( PRG_NAME, "error: " + e.to_s )
end
begin
Util.check_file_for_writability( output )
Util.fatal_error( PRG_NAME, "error: " + e.to_s )
end
begin
Util.check_file_for_writability( output )
puts( " options: -" + INPUT_TYPE_OPTION + "=<input type>: f for fasta, p for phylip selex type" )
puts( " -" + OUTPUT_TYPE_OPTION + "=<output type>: f for fasta, n for nexus, p for phylip sequential (default)" )
puts( " -" + MAXIMAL_NAME_LENGTH_OPTION + "=<n>: n=maximal name length (default for phylip 10, for fasta: unlimited )" )
puts( " options: -" + INPUT_TYPE_OPTION + "=<input type>: f for fasta, p for phylip selex type" )
puts( " -" + OUTPUT_TYPE_OPTION + "=<output type>: f for fasta, n for nexus, p for phylip sequential (default)" )
puts( " -" + MAXIMAL_NAME_LENGTH_OPTION + "=<n>: n=maximal name length (default for phylip 10, for fasta: unlimited )" )
puts( " -" + WIDTH_OPTION + "=<n>: n=width (fasta output only, default is 60)" )
puts( " -" + CLEAN_UP_SEQ_OPTION + ": clean up sequences" )
puts( " -" + REMOVE_GAP_COLUMNS_OPTION + ": remove gap columns" )
puts( " -" + WIDTH_OPTION + "=<n>: n=width (fasta output only, default is 60)" )
puts( " -" + CLEAN_UP_SEQ_OPTION + ": clean up sequences" )
puts( " -" + REMOVE_GAP_COLUMNS_OPTION + ": remove gap columns" )