2 # = lib/evo/apps/msa_processor.rb - MsaProcessor class
4 # Copyright:: Copyright (C) 2006-2007 Christian M. Zmasek
5 # License:: GNU Lesser General Public License (LGPL)
7 # $Id: msa_processor.rb,v 1.33 2010/12/13 19:00:10 cmzmasek Exp $
12 require 'lib/evo/util/constants'
13 require 'lib/evo/util/util'
14 require 'lib/evo/util/command_line_arguments'
15 require 'lib/evo/msa/msa_factory'
16 require 'lib/evo/io/msa_io'
17 require 'lib/evo/io/writer/phylip_sequential_writer'
18 require 'lib/evo/io/writer/nexus_writer'
19 require 'lib/evo/io/writer/fasta_writer'
20 require 'lib/evo/io/parser/fasta_parser'
21 require 'lib/evo/io/parser/general_msa_parser'
22 require 'lib/evo/io/writer/msa_writer'
29 PRG_DESC = "processing of multiple sequence alignments"
31 WWW = "https://sites.google.com/site/cmzmasek/home/software/forester"
33 NAME_LENGTH_DEFAULT = 10
34 WIDTH_DEFAULT_FASTA = 60
35 INPUT_TYPE_OPTION = "i"
36 OUTPUT_TYPE_OPTION = "o"
37 MAXIMAL_NAME_LENGTH_OPTION = "n"
38 DIE_IF_NAME_TOO_LONG = "d"
40 CLEAN_UP_SEQ_OPTION = "c"
41 REM_RED_OPTION = "rem_red"
42 REMOVE_GAP_COLUMNS_OPTION = "rgc"
43 REMOVE_GAP_ONLY_COLUMNS = "rgoc"
44 REMOVE_COLUMNS_GAP_RATIO_OPTION = "rr"
45 REMOVE_ALL_GAP_CHARACTERS_OPTION = "rg"
46 REMOVE_ALL_SEQUENCES_LISTED_OPTION = "r"
47 KEEP_ONLY_SEQUENCES_LISTED_OPTION = "k"
49 KEEP_MATCHING_SEQUENCES_OPTION = "mk"
50 REMOVE_MATCHING_SEQUENCES_OPTION = "mr"
53 REMOVE_SEQS_GAP_RATIO_OPTION = "rsgr"
54 REMOVE_SEQS_NON_GAP_LENGTH_OPTION = "rsl"
56 SPLIT_BY_OS = "split_by_os"
57 LOG_SUFFIX = "_msa_pro.log"
58 HELP_OPTION_1 = "help"
61 @input_format_set = false
62 @output_format_set = false
65 @name_length = NAME_LENGTH_DEFAULT
66 @name_length_set = false
67 @width = WIDTH_DEFAULT_FASTA # fasta only
71 @clean = false # phylip only
74 @rg = false # fasta only
76 @die_if_name_too_long = false
80 @remove_matching = nil
95 Util.print_program_information( PRG_NAME,
102 if ( ARGV == nil || ARGV.length < 1 )
103 Util.print_message( PRG_NAME, "Illegal number of arguments" )
109 cla = CommandLineArguments.new( ARGV )
110 rescue ArgumentError => e
111 Util.fatal_error( PRG_NAME, "Error: " + e.to_s, STDOUT )
114 if ( cla.is_option_set?( HELP_OPTION_1 ) ||
115 cla.is_option_set?( HELP_OPTION_2 ) )
120 if ( cla.get_number_of_files != 2 || ARGV.length < 2 )
121 Util.print_message( PRG_NAME, "Illegal number of arguments" )
126 allowed_opts = Array.new
127 allowed_opts.push( INPUT_TYPE_OPTION )
128 allowed_opts.push( OUTPUT_TYPE_OPTION )
129 allowed_opts.push( MAXIMAL_NAME_LENGTH_OPTION )
130 allowed_opts.push( WIDTH_OPTION )
131 allowed_opts.push( CLEAN_UP_SEQ_OPTION )
132 allowed_opts.push( REMOVE_GAP_COLUMNS_OPTION )
133 allowed_opts.push( REMOVE_GAP_ONLY_COLUMNS )
134 allowed_opts.push( REMOVE_COLUMNS_GAP_RATIO_OPTION )
135 allowed_opts.push( REMOVE_ALL_GAP_CHARACTERS_OPTION )
136 allowed_opts.push( REMOVE_ALL_SEQUENCES_LISTED_OPTION )
137 allowed_opts.push( KEEP_ONLY_SEQUENCES_LISTED_OPTION )
138 allowed_opts.push( TRIM_OPTION )
139 allowed_opts.push( REMOVE_SEQS_GAP_RATIO_OPTION )
140 allowed_opts.push( REMOVE_SEQS_NON_GAP_LENGTH_OPTION )
141 allowed_opts.push( SPLIT )
142 allowed_opts.push( SPLIT_BY_OS )
143 allowed_opts.push( REM_RED_OPTION )
144 allowed_opts.push( KEEP_MATCHING_SEQUENCES_OPTION )
145 allowed_opts.push( REMOVE_MATCHING_SEQUENCES_OPTION )
146 allowed_opts.push( DIE_IF_NAME_TOO_LONG )
148 disallowed = cla.validate_allowed_options_as_str( allowed_opts )
149 if ( disallowed.length > 0 )
150 Util.fatal_error( PRG_NAME,
151 "unknown option(s): " + disallowed )
154 input = cla.get_file_name( 0 )
155 output = cla.get_file_name( 1 )
157 analyze_command_line( cla )
160 Util.check_file_for_readability( input )
162 Util.fatal_error( PRG_NAME, "error: " + e.to_s )
166 Util.check_file_for_writability( output )
168 Util.fatal_error( PRG_NAME, "error: " + e.to_s )
172 set_pi_output( false )
173 set_fasta_output( true )
174 set_nexus_output( false )
177 if ( !@input_format_set )
180 fasta_like = Util.looks_like_fasta?( input )
181 rescue ArgumentError => e
182 Util.fatal_error( PRG_NAME, "error: " + e.to_s )
184 @fasta_input = fasta_like
185 @phylip_input = !fasta_like
186 if ( !@output_format_set )
187 @fasta_output = fasta_like
188 @pi_output = !fasta_like
189 @nexus_output = false
193 ld = Constants::LINE_DELIMITER
194 log = PRG_NAME + " " + PRG_VERSION + " [" + PRG_DATE + "]" + " LOG" + ld
196 log << "Date/time: " + now.to_s + ld
199 puts( "Input alignment : " + input )
200 log << "Input alignment : " + input + ld
201 puts( "Output alignment : " + output )
202 log << "Output alignment : " + output + ld
204 puts( "Input is : Phylip, or something like it" )
205 log << "Input is : Phylip, or something like it" + ld
206 elsif ( @fasta_input )
207 puts( "Input is : Fasta" )
208 log << "Input is : Fasta" + ld
211 puts( "Max col gap ratio: " + @rgr.to_s )
212 log << "Max col gap ratio: " + @rgr.to_s + ld
214 puts( "Remove gap colums" )
215 log << "Remove gap colums" + ld
217 puts( "Remove gap only colums" )
218 log << "Remove gap only colums" + ld
221 puts( "Clean up : true" )
222 log << "Clean up : true" + ld
226 puts( "Output is : Phylip interleaved" )
227 log << "Output is : Phylip interleaved" + ld
228 elsif ( @fasta_output )
229 puts( "Output is : Fasta" )
230 log << "Output is : Fasta" + ld
232 puts( "Width : " + @width.to_s )
233 log << "Width : " + @width.to_s + ld
236 puts( "Remove all gap characters (alignment is destroyed)" )
237 log << "Remove all gap characters (alignment is destroyed)" + ld
239 elsif ( @nexus_output )
240 puts( "Output is : Nexus" )
241 log << "Output is : Nexus" + ld
243 if ( @name_length_set || !@fasta_output )
244 puts( "Max name length : " + @name_length.to_s )
245 log << "Max name length : " + @name_length.to_s + ld
248 puts( "Remove sequences for which the gap ratio > " + @rsgr.to_s )
249 log << "Remove sequences for which the gap ratio > " + @rsgr.to_s + ld
252 puts( "Remove sequences with less than " + @rsl.to_s + " non-gap characters" )
253 log << "Remove sequences with less than " + @rsl.to_s + " non-gap characters" + ld
256 puts( "Remove sequences listed in: " + @seqs_name_file )
257 log << "Remove sequences listed in: " + @seqs_name_file + ld
259 puts( "Keep only sequences listed in: " + @seqs_name_file )
260 log << "Keep only sequences listed in: " + @seqs_name_file + ld
263 puts( "Keep only columns from: "+ @first.to_s + " to " + @last.to_s )
264 log << "Keep only columns from: "+ @first.to_s + " to " + @last.to_s + ld
267 puts( "Remove redundant sequences: true" )
268 log << "Remove redundant sequences: true" + ld
271 puts( "Split by OS : true" )
272 log << "Split : true" + ld
275 puts( "Split : " + @split.to_s )
276 log << "Split : " + @split.to_s + ld
286 msa = f.create_msa_from_file( input, GeneralMsaParser.new() )
287 elsif ( @fasta_input )
288 msa = f.create_msa_from_file( input, FastaParser.new() )
290 rescue Exception => e
291 Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )
294 if ( msa.is_aligned() )
295 Util.print_message( PRG_NAME, "Length of original alignment : " + msa.get_length.to_s )
296 log << "Length of original alignment : " + msa.get_length.to_s + ld
297 gp = msa.calculate_gap_proportion
298 Util.print_message( PRG_NAME, "Gap-proportion of original alignment : " + gp.to_s )
299 log << "Gap-proportion of original alignment : " + gp.to_s + ld
301 Util.print_message( PRG_NAME, "Input is not aligned" )
302 log << "Input is not aligned" + ld
305 all_names = Set.new()
306 for i in 0 ... msa.get_number_of_seqs()
307 current_name = msa.get_sequence( i ).get_name
308 if all_names.include?( current_name )
309 Util.print_warning_message( PRG_NAME, "sequence name [" + current_name + "] is not unique" )
311 all_names.add( current_name )
317 if ( @remove_seqs || @keep_seqs )
318 names = Util.file2array( @seqs_name_file, true )
319 if ( names == nil || names.length() < 1 )
320 error_msg = "file \"" + @seqs_name_file.to_s + "\" appears empty"
321 Util.fatal_error( PRG_NAME, error_msg )
326 for i in 0 ... names.length()
327 to_delete = msa.find_by_name( names[ i ], true, false )
328 if ( to_delete.length() < 1 )
329 error_msg = "sequence name \"" + names[ i ] + "\" not found"
330 Util.fatal_error( PRG_NAME, error_msg )
331 elsif ( to_delete.length() > 1 )
332 error_msg = "sequence name \"" + names[ i ] + "\" is not unique"
333 Util.fatal_error( PRG_NAME, error_msg )
335 msa.remove_sequence!( to_delete[ 0 ] )
339 Util.print_message( PRG_NAME, "Removed " + c.to_s + " sequences" )
340 log << "Removed " + c.to_s + " sequences" + ld
345 for j in 0 ... msa.get_number_of_seqs()
346 if ( names.include?( msa.get_sequence( j ).get_name() ) )
347 msa_new.add_sequence( msa.get_sequence( j ) )
354 Util.print_message( PRG_NAME, "Kept " + k.to_s + " sequences" )
355 log << "Kept " + k.to_s + " sequences" + ld
356 Util.print_message( PRG_NAME, "Removed " + r.to_s + " sequences" )
357 log << "removed " + r.to_s + " sequences" + ld
362 msa.trim!( @first, @last )
365 msa.remove_gap_columns_w_gap_ratio!( @rgr )
367 msa.remove_gap_columns!()
369 msa.remove_gap_only_columns!()
372 n = msa.get_number_of_seqs()
373 removed = msa.remove_sequences_by_gap_ratio!( @rsgr )
374 k = msa.get_number_of_seqs()
376 Util.print_message( PRG_NAME, "Kept " + k.to_s + " sequences" )
377 log << "Kept " + k.to_s + " sequences" + ld
378 Util.print_message( PRG_NAME, "Removed " + r.to_s + " sequences" )
379 log << "Removed " + r.to_s + " sequences:" + ld
380 removed.each { | seq_name |
381 log << " " + seq_name + ld
385 n = msa.get_number_of_seqs()
386 removed = msa.remove_sequences_by_non_gap_length!( @rsl )
387 k = msa.get_number_of_seqs()
389 Util.print_message( PRG_NAME, "Kept " + k.to_s + " sequences" )
390 log << "Kept " + k.to_s + " sequences" + ld
391 Util.print_message( PRG_NAME, "Removed " + r.to_s + " sequences" )
392 log << "Removed " + r.to_s + " sequences:" + ld
393 removed.each { | seq_name |
394 log << " " + seq_name + ld
397 if ( @keep_matching )
398 n = msa.get_number_of_seqs
399 to_be_removed = Set.new
401 seq = msa.get_sequence( ii )
402 if !seq.get_name.downcase.index( @keep_matching.downcase )
403 to_be_removed.add( ii )
406 to_be_removed_ary = to_be_removed.to_a.sort.reverse
407 to_be_removed_ary.each { | index |
408 msa.remove_sequence!( index )
412 if ( @remove_matching )
413 n = msa.get_number_of_seqs
414 to_be_removed = Set.new
417 seq = msa.get_sequence( iii )
419 if seq.get_name.downcase.index( @remove_matching.downcase )
420 to_be_removed.add( iii )
423 to_be_removed_ary = to_be_removed.to_a.sort.reverse
424 to_be_removed_ary.each { | index |
425 msa.remove_sequence!( index )
432 msa_hash = msa.split_by_os(true)
436 w = PhylipSequentialWriter.new()
438 w.set_max_name_length( @name_length )
439 elsif( @fasta_output )
440 w = FastaWriter.new()
441 w.set_line_width( @width )
443 w.remove_gap_chars( true )
444 Util.print_warning_message( PRG_NAME, "removing gap character, the output is likely to become unaligned" )
445 log << "removing gap character, the output is likely to become unaligned" + ld
448 if ( @name_length_set )
449 w.set_max_name_length( @name_length )
451 elsif( @nexus_output )
452 w = NexusWriter.new()
454 w.set_max_name_length( @name_length )
456 msa_hash.each do |os, msa|
457 my_os = os.gsub(' ', '_').gsub('/', '_').gsub('(', '_').gsub(')', '_')
458 io.write_to_file( msa, output + '_' + my_os, w )
461 Util.print_message( PRG_NAME, "wrote " + msa_hash.length.to_s + " files" )
462 log << "wrote " + msa_hash.length.to_s + " files" + ld
463 rescue Exception => e
464 Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )
469 msas = msa.split( @split, true )
473 w = PhylipSequentialWriter.new()
475 w.set_max_name_length( @name_length )
476 elsif( @fasta_output )
477 w = FastaWriter.new()
478 w.set_line_width( @width )
480 w.remove_gap_chars( true )
481 Util.print_warning_message( PRG_NAME, "removing gap character, the output is likely to become unaligned" )
482 log << "removing gap character, the output is likely to become unaligned" + ld
485 if ( @name_length_set )
486 w.set_max_name_length( @name_length )
488 elsif( @nexus_output )
489 w = NexusWriter.new()
491 w.set_max_name_length( @name_length )
496 io.write_to_file( m, output + "_" + i.to_s, w )
498 Util.print_message( PRG_NAME, "wrote " + msas.length.to_s + " files" )
499 log << "wrote " + msas.length.to_s + " files" + ld
500 rescue Exception => e
501 Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )
504 rescue Exception => e
505 Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )
508 if (@split <= 0) && (!@split_by_os)
511 if ( msa.is_aligned() )
512 Util.print_message( PRG_NAME, "Length of processed alignment : " + msa.get_length.to_s )
513 log << "Length of processed alignment : " + msa.get_length.to_s + ld
514 gp = msa.calculate_gap_proportion
515 Util.print_message( PRG_NAME, "Gap-proportion of processed alignment: " + gp.to_s )
516 log << "Gap-proportion of processed alignment: " + gp.to_s + ld
522 for s in 0 ... msa.get_number_of_seqs
523 seq = msa.get_sequence( s )
534 avg = sum / msa.get_number_of_seqs
535 Util.print_message( PRG_NAME, "Output is not aligned" )
536 log << "Output is not aligned" + ld
537 Util.print_message( PRG_NAME, "Shortest sequence : " + min.to_s )
538 log << "Shortest sequence : " + min.to_s + ld
539 Util.print_message( PRG_NAME, "Longest sequence : " + max.to_s )
540 log << "Longest sequence : " + max.to_s + ld
541 Util.print_message( PRG_NAME, "Average length : " + avg.to_s )
542 log << "Average length : " + avg.to_s + ld
548 removed = msa.remove_redundant_sequences!( true, false )
550 identicals = msa.get_identical_seqs_detected
551 log << "the following " + identicals.size.to_s + " sequences are identical:" + ld
552 identicals.each { | identical |
553 log << identical + ld
555 log << "ignoring the following " + removed.size.to_s + " redundant sequences:" + ld
556 removed.each { | seq_name |
559 Util.print_message( PRG_NAME, "will store " + msa.get_number_of_seqs.to_s + " non-redundant sequences" )
560 log << "will store " + msa.get_number_of_seqs.to_s + " non-redundant sequences" + ld
569 w = PhylipSequentialWriter.new()
571 w.set_max_name_length( @name_length )
572 w.set_exception_if_name_too_long( @die_if_name_too_long )
573 elsif( @fasta_output )
574 w = FastaWriter.new()
575 w.set_line_width( @width )
577 w.remove_gap_chars( true )
578 Util.print_warning_message( PRG_NAME, "removing gap characters, the output is likely to become unaligned" )
579 log << "removing gap character, the output is likely to become unaligned" + ld
582 if ( @name_length_set )
583 w.set_max_name_length( @name_length )
584 w.set_exception_if_name_too_long( @die_if_name_too_long )
586 elsif( @nexus_output )
587 w = NexusWriter.new()
589 w.set_max_name_length( @name_length )
590 w.set_exception_if_name_too_long( @die_if_name_too_long )
594 io.write_to_file( msa, output, w )
595 rescue Exception => e
596 Util.fatal_error( PRG_NAME, "error: " + e.to_s )
599 Util.print_message( PRG_NAME, "Number of sequences in output : " + msa.get_number_of_seqs.to_s )
600 log << "Number of sequences in output : " + msa.get_number_of_seqs.to_s + ld
603 f = File.open( output + LOG_SUFFIX, 'a' )
606 rescue Exception => e
607 Util.fatal_error( PRG_NAME, "error: " + e.to_s )
611 Util.print_message( PRG_NAME, "OK" )
619 for i in 0 ... msa.get_number_of_seqs
620 name = msa.get_sequence( i ).get_name
623 sorted_ary = names.to_a.sort
625 sorted_ary.each { | seq_name |
626 seq = msa.get_sequence( msa.find_by_name( seq_name, true, false )[ 0 ] )
627 new_msa.add_sequence( seq )
632 def set_fasta_input( fi = true )
634 @input_format_set = true
637 def set_phylip_input( pi = true )
639 @input_format_set = true
642 def set_name_length( i )
644 @name_length_set = true
651 def set_fasta_output( fo = true )
653 @output_format_set = true
656 def set_pi_output( pso = true )
658 @output_format_set = true
661 def set_nexus_output( nexus = true )
662 @nexus_output = nexus
663 @output_format_set = true
666 def set_clean( c = true )
670 def set_remove_gap_columns( rgc = true )
674 def set_remove_gap_only_columns( rgoc = true )
678 def set_remove_gaps( rg = true )
682 def set_remove_gap_ratio( rgr )
686 def set_remove_seqs_gap_ratio( rsgr )
690 def set_remove_seqs_min_non_gap_length( rsl )
694 def set_remove_seqs( file )
695 @seqs_name_file = file
700 def set_keep_seqs( file )
701 @seqs_name_file = file
706 def set_trim( first, last )
712 def set_remove_matching( remove )
713 @remove_matching = remove
716 def set_keep_matching( keep )
717 @keep_matching = keep
720 def set_rem_red( rr )
728 @clean = false # phylip only
731 @rg = false # fasta only
735 @seqs_name_file = nil
744 def set_split_by_os()
747 @clean = false # phylip only
750 @rg = false # fasta only
754 @seqs_name_file = nil
762 def analyze_command_line( cla )
763 if ( cla.is_option_set?( INPUT_TYPE_OPTION ) )
765 type = cla.get_option_value( INPUT_TYPE_OPTION )
767 set_phylip_input( true )
768 set_fasta_input( false )
769 elsif ( type == "f" )
770 set_fasta_input( true )
771 set_phylip_input( false )
773 rescue ArgumentError => e
774 Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )
777 if ( cla.is_option_set?( OUTPUT_TYPE_OPTION ) )
779 type = cla.get_option_value( OUTPUT_TYPE_OPTION )
781 set_pi_output( true )
782 set_fasta_output( false )
783 set_nexus_output( false )
784 elsif ( type == "f" )
785 set_pi_output( false )
786 set_fasta_output( true )
787 set_nexus_output( false )
788 elsif ( type == "n" )
789 set_pi_output( false )
790 set_fasta_output( false )
791 set_nexus_output( true )
793 rescue ArgumentError => e
794 Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )
797 if ( cla.is_option_set?( MAXIMAL_NAME_LENGTH_OPTION ) )
799 l = cla.get_option_value_as_int( MAXIMAL_NAME_LENGTH_OPTION )
801 rescue ArgumentError => e
802 Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )
805 if ( cla.is_option_set?( WIDTH_OPTION ) )
807 w = cla.get_option_value_as_int( WIDTH_OPTION )
809 rescue ArgumentError => e
810 Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )
813 if ( cla.is_option_set?( CLEAN_UP_SEQ_OPTION ) )
816 if ( cla.is_option_set?( REMOVE_GAP_COLUMNS_OPTION ) )
817 set_remove_gap_columns( true )
819 if ( cla.is_option_set?( REM_RED_OPTION ) )
822 if ( cla.is_option_set?( REMOVE_GAP_ONLY_COLUMNS ) )
823 set_remove_gap_only_columns( true )
825 if ( cla.is_option_set?( REMOVE_ALL_GAP_CHARACTERS_OPTION ) )
826 set_remove_gaps( true )
828 if ( cla.is_option_set?( REMOVE_COLUMNS_GAP_RATIO_OPTION ) )
830 f = cla.get_option_value_as_float( REMOVE_COLUMNS_GAP_RATIO_OPTION )
831 set_remove_gap_ratio( f )
832 rescue ArgumentError => e
833 Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )
836 if ( cla.is_option_set?( REMOVE_ALL_SEQUENCES_LISTED_OPTION ) )
838 s = cla.get_option_value( REMOVE_ALL_SEQUENCES_LISTED_OPTION )
840 rescue ArgumentError => e
841 Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )
844 if ( cla.is_option_set?( KEEP_ONLY_SEQUENCES_LISTED_OPTION ) )
846 s = cla.get_option_value( KEEP_ONLY_SEQUENCES_LISTED_OPTION )
848 rescue ArgumentError => e
849 Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )
852 if ( cla.is_option_set?( TRIM_OPTION ) )
854 s = cla.get_option_value( TRIM_OPTION )
855 if ( s =~ /(\d+)-(\d+)/ )
856 set_trim( $1.to_i(), $2.to_i() )
858 puts( "illegal argument" )
862 rescue ArgumentError => e
863 Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )
866 if ( cla.is_option_set?( REMOVE_SEQS_GAP_RATIO_OPTION ) )
868 f = cla.get_option_value_as_float( REMOVE_SEQS_GAP_RATIO_OPTION )
869 set_remove_seqs_gap_ratio( f )
870 rescue ArgumentError => e
871 Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )
874 if ( cla.is_option_set?( REMOVE_SEQS_NON_GAP_LENGTH_OPTION ) )
876 f = cla.get_option_value_as_int( REMOVE_SEQS_NON_GAP_LENGTH_OPTION )
877 set_remove_seqs_min_non_gap_length( f )
878 rescue ArgumentError => e
879 Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )
882 if cla.is_option_set?( SPLIT_BY_OS )
885 rescue ArgumentError => e
886 Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )
888 elsif ( cla.is_option_set?( SPLIT ) )
890 s = cla.get_option_value_as_int( SPLIT )
892 rescue ArgumentError => e
893 Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )
896 if ( cla.is_option_set?( REMOVE_MATCHING_SEQUENCES_OPTION ) )
898 s = cla.get_option_value( REMOVE_MATCHING_SEQUENCES_OPTION )
899 set_remove_matching( s )
900 rescue ArgumentError => e
901 Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )
904 if ( cla.is_option_set?( KEEP_MATCHING_SEQUENCES_OPTION ) )
906 s = cla.get_option_value( KEEP_MATCHING_SEQUENCES_OPTION )
907 set_keep_matching( s )
908 rescue ArgumentError => e
909 Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )
912 if ( cla.is_option_set?( DIE_IF_NAME_TOO_LONG ) )
913 @die_if_name_too_long = true
922 puts( " " + PRG_NAME + ".rb [options] <input alignment> <output>" )
924 puts( " options: -" + INPUT_TYPE_OPTION + "=<input type>: f for fasta, p for phylip selex type" )
925 puts( " -" + OUTPUT_TYPE_OPTION + "=<output type>: f for fasta, n for nexus, p for phylip sequential (default)" )
926 puts( " -" + MAXIMAL_NAME_LENGTH_OPTION + "=<n>: n=maximal name length (default for phylip 10, for fasta: unlimited )" )
927 puts( " -" + DIE_IF_NAME_TOO_LONG + ": die if sequence name too long" )
928 puts( " -" + WIDTH_OPTION + "=<n>: n=width (fasta output only, default is 60)" )
929 puts( " -" + CLEAN_UP_SEQ_OPTION + ": clean up sequences" )
930 puts( " -" + REMOVE_GAP_COLUMNS_OPTION + ": remove gap columns" )
931 puts( " -" + REMOVE_GAP_ONLY_COLUMNS + ": remove gap-only columns" )
932 puts( " -" + REMOVE_COLUMNS_GAP_RATIO_OPTION + "=<n>: remove columns for which ( seqs with gap / number of sequences > n )" )
933 puts( " -" + REMOVE_ALL_GAP_CHARACTERS_OPTION + ": remove all gap characters (destroys alignment, fasta output only)" )
934 puts( " -" + REMOVE_ALL_SEQUENCES_LISTED_OPTION + "=<file>: remove all sequences listed in file" )
935 puts( " -" + KEEP_ONLY_SEQUENCES_LISTED_OPTION + "=<file>: keep only sequences listed in file" )
936 puts( " -" + TRIM_OPTION + "=<first>-<last>: remove columns before first and after last" )
937 puts( " -" + REMOVE_SEQS_GAP_RATIO_OPTION + "=<n>: remove sequences for which the gap ratio > n (after column operations)" )
938 puts( " -" + REMOVE_SEQS_NON_GAP_LENGTH_OPTION + "=<n> remove sequences with less than n non-gap characters (after column operations)" )
939 puts( " -" + REMOVE_MATCHING_SEQUENCES_OPTION + "=<s> remove all sequences with names containing s" )
940 puts( " -" + KEEP_MATCHING_SEQUENCES_OPTION + "=<s> keep only sequences with names containing s" )
941 puts( " -" + SPLIT + "=<n> split a fasta file into n files of equal number of sequences (expect for " )
942 puts( " last one), cannot be used with other options" )
943 puts( " -" + REM_RED_OPTION + ": remove redundant sequences" )
947 end # class MsaProcessor