2 # = lib/evo/msa/msa.rb - Msa class
4 # Copyright:: Copyright (C) 2006-2007 Christian M. Zmasek
5 # License:: GNU Lesser General Public License (LGPL)
7 # $Id: msa.rb,v 1.11 2009/01/03 00:42:08 cmzmasek Exp $
11 require 'lib/evo/util/constants'
12 require 'lib/evo/util/util'
13 require 'lib/evo/sequence/sequence'
20 @sequences = Array.new
21 @identical_seqs_detected = Array.new
25 def add_sequence( sequence )
26 @sequences.push( sequence )
29 def add( name, molecular_sequence_str )
30 add_sequence( Sequence.new( name, molecular_sequence_str ) )
33 def get_sequence( index )
34 if ( index < 0 || index > get_number_of_seqs() - 1 )
35 error_msg = "attempt to get sequence " <<
36 index.to_s << " in alignment of " << get_number_of_seqs().to_s <<
38 raise ArgumentError, error_msg
40 return @sequences[ index ]
43 def remove_sequence!( index )
44 if ( index < 0 || index > get_number_of_seqs() - 1 )
45 error_msg = "attempt to remove sequence " <<
46 index.to_s << " in alignment of " << get_number_of_seqs().to_s <<
48 raise ArgumentError, error_msg
50 @sequences.delete_at( index )
53 def get_identical_seqs_detected
54 @identical_seqs_detected
59 if ( get_number_of_seqs < 1 )
62 l = @sequences[ 0 ].get_length()
63 for i in 0 ... get_number_of_seqs()
64 if ( get_sequence( i ).get_length() != l )
72 def find_by_name( name, case_sensitive, partial_match )
74 for i in 0 ... get_number_of_seqs()
75 current_name = get_sequence( i ).get_name()
77 current_name = current_name.downcase
80 if current_name == name ||
81 ( partial_match && current_name.include?( name ) )
88 def find_by_name_start( name, case_sensitive )
90 for i in 0 ... get_number_of_seqs()
91 get_sequence( i ).get_name() =~ /^\s*(\S+)/
94 current_name = current_name.downcase
97 if ( current_name == name )
104 def has?( name, case_sensitive = true, partial_match = false )
105 for i in 0 ... get_number_of_seqs()
106 current_name = get_sequence( i ).get_name()
108 current_name = current_name.downcase
111 if current_name == name ||
112 ( partial_match && current_name.include?( name ) )
119 # throws ArgumentError
120 def get_by_name( name, case_sensitive = true, partial_match = false )
121 indices = find_by_name( name, case_sensitive, partial_match )
122 if ( indices.length > 1 )
123 error_msg = "\"" + name + "\" not unique"
124 raise ArgumentError, error_msg
125 elsif ( indices.length < 1 )
126 error_msg = "\"" + name + "\" not found"
127 raise ArgumentError, error_msg
129 get_sequence( indices[ 0 ] )
132 # throws ArgumentError
133 def get_by_name_start( name, case_sensitive = true )
134 indices = find_by_name_start( name, case_sensitive )
135 if ( indices.length > 1 )
136 error_msg = "\"" + name + "\" not unique"
137 raise ArgumentError, error_msg
138 elsif ( indices.length < 1 )
139 error_msg = "\"" + name + "\" not found"
140 raise ArgumentError, error_msg
142 get_sequence( indices[ 0 ] )
146 def get_sub_alignment( seq_numbers )
148 for i in 0 ... seq_numbers.length()
149 msa.add_sequence( get_sequence( seq_numbers[ i ] ).copy() )
154 def get_number_of_seqs()
160 error_msg = "attempt to get length of unaligned msa"
161 raise StandardError, error_msg, caller
163 if ( get_number_of_seqs() < 1 )
166 @sequences[ 0 ].get_length()
172 for i in 0...get_number_of_seqs()
173 s += @sequences[ i ].to_str + Constants::LINE_DELIMITER
178 def print_overlap_diagram( min_overlap = 1, io = STDOUT, max_name_length = 10 )
180 error_msg = "attempt to get overlap diagram of unaligned msa"
181 raise StandardError, error_msg, caller
183 for i in 0 ... get_number_of_seqs()
184 io.print( Util.normalize_seq_name( get_sequence( i ).get_name(), max_name_length ) )
185 for j in 0 ... get_number_of_seqs()
189 if overlap?( i, j, min_overlap )
196 io.print( Evoruby::Constants::LINE_DELIMITER )
200 #returns array of Msa with an overlap of min_overlap
201 def split_into_overlapping_msa( min_overlap = 1 )
203 error_msg = "attempt to split into overlapping msas of unaligned msa"
204 raise StandardError, error_msg, caller
207 bins = get_overlaps( min_overlap )
208 for i in 0 ... bins.length
209 msas.push( get_sub_alignment( bins[ i ] ) )
214 def overlap?( index_1, index_2, min_overlap = 1 )
215 seq_1 = get_sequence( index_1 )
216 seq_2 = get_sequence( index_2 )
218 for i in 0...seq_1.get_length()
219 if !Util.is_aa_gap_character?( seq_1.get_character_code( i ) ) &&
220 !Util.is_aa_gap_character?( seq_2.get_character_code( i ) )
222 if overlap_count >= min_overlap
230 def calculate_overlap( index_1, index_2 )
231 seq_1 = get_sequence( index_1 )
232 seq_2 = get_sequence( index_2 )
234 for i in 0...seq_1.get_length
235 if !Util.is_aa_gap_character?( seq_1.get_character_code( i ) ) &&
236 !Util.is_aa_gap_character?( seq_2.get_character_code( i ) )
243 def calculate_identities( index_1, index_2 )
244 seq_1 = get_sequence( index_1 )
245 seq_2 = get_sequence( index_2 )
247 for i in 0...seq_1.get_length
248 if !Util.is_aa_gap_character?( seq_1.get_character_code( i ) ) &&
249 !Util.is_aa_gap_character?( seq_2.get_character_code( i ) ) &&
250 seq_1.get_character_code( i ) != 63 &&
251 ( seq_1.get_residue( i ).downcase() ==
252 seq_2.get_residue( i ).downcase() )
253 identities_count += 1
259 def remove_gap_only_columns!()
260 remove_columns!( get_gap_only_columns() )
263 def remove_gap_columns!()
264 remove_columns!( get_gap_columns() )
267 # removes columns for which seqs with gap / number of sequences > gap_ratio
268 def remove_gap_columns_w_gap_ratio!( gap_ratio )
269 remove_columns!( get_gap_columns_w_gap_ratio( gap_ratio ) )
273 def remove_sequences_by_gap_ratio!( gap_ratio )
275 error_msg = "attempt to remove sequences by gap ratio on unaligned msa"
276 raise StandardError, error_msg, caller
278 n = get_number_of_seqs
281 if ( get_sequence( ( n - 1 ) - s ).get_gap_ratio() > gap_ratio )
282 if ( Evoruby::Constants::VERBOSE )
283 puts( "removed: " + get_sequence( ( n - 1 ) - s ).get_name )
285 removed << get_sequence( ( n - 1 ) - s ).get_name
286 remove_sequence!( ( n - 1 ) - s )
293 def remove_redundant_sequences!( consider_taxonomy = false, verbose = false )
294 n = get_number_of_seqs
296 to_be_removed = Set.new
297 @identical_seqs_detected = Array.new
298 for i in 0 ... ( n - 1 )
299 for j in ( i + 1 ) ... n
300 if !to_be_removed.include?( i ) && !to_be_removed.include?( j )
301 if !consider_taxonomy ||
302 ( ( get_sequence( i ).get_taxonomy == nil && get_sequence( j ).get_taxonomy == nil ) ||
303 ( get_sequence( i ).get_taxonomy == get_sequence( j ).get_taxonomy ) )
304 if Util.clean_seq_str( get_sequence( i ).get_sequence_as_string ) ==
305 Util.clean_seq_str( get_sequence( j ).get_sequence_as_string )
306 to_be_removed.add( j )
310 if get_sequence( i ).get_taxonomy != nil
311 tax_i = get_sequence( i ).get_taxonomy.get_name
313 if get_sequence( j ).get_taxonomy != nil
314 tax_j = get_sequence( j ).get_taxonomy.get_name
316 identical_pair = get_sequence( i ).get_name + " [#{tax_i}] == " + get_sequence( j ).get_name + " [#{tax_j}]"
317 @identical_seqs_detected.push( identical_pair )
327 to_be_removed_ary = to_be_removed.to_a.sort.reverse
329 to_be_removed_ary.each { | index |
330 removed.push( get_sequence( index ).get_name )
331 remove_sequence!( index )
337 def remove_sequences_by_non_gap_length!( min_non_gap_length )
339 error_msg = "attempt to remove sequences by non gap length on unaligned msa"
340 raise StandardError, error_msg, caller
342 n = get_number_of_seqs
346 if ( ( l - get_sequence( ( n - 1 ) - s ).get_gap_length ) < min_non_gap_length )
347 if ( Evoruby::Constants::VERBOSE )
348 puts( "removed: " + get_sequence( ( n - 1 ) - s ).get_name )
350 removed << get_sequence( ( n - 1 ) - s ).get_name
351 remove_sequence!( ( n - 1 ) - s )
357 def trim!( first, last )
359 for i in 0 ... get_length()
360 if ( i < first || i > last )
364 remove_columns!( cols )
367 def get_gap_only_columns()
369 error_msg = "attempt to get gap only columns of unaligned msa"
370 raise StandardError, error_msg, caller
373 for c in 0 ... get_length
374 nogap_char_found = false
375 for s in 0 ... get_number_of_seqs
376 unless Util.is_aa_gap_character?( get_sequence( s ).get_character_code( c ) )
377 nogap_char_found = true
381 unless nogap_char_found
388 def calculate_gap_proportion()
390 error_msg = "attempt to get gap only columns of unaligned msa"
391 raise StandardError, error_msg, caller
395 for c in 0 ... get_length
396 for s in 0 ... get_number_of_seqs
397 total_sum = total_sum + 1
398 if Util.is_aa_gap_character?( get_sequence( s ).get_character_code( c ) )
399 gap_sum = gap_sum + 1
404 return gap_sum / total_sum
407 def get_gap_columns()
409 error_msg = "attempt to get gap columns of unaligned msa"
410 raise StandardError, error_msg, caller
413 for c in 0 ... get_length
414 gap_char_found = false
415 for s in 0 ... get_number_of_seqs
416 if Util.is_aa_gap_character?( get_sequence( s ).get_character_code( c ) )
417 gap_char_found = true
428 # gap_ratio = seqs with gap / number of sequences
429 # returns column indices for which seqs with gap / number of sequences > gap_ratio
430 def get_gap_columns_w_gap_ratio( gap_ratio )
432 error_msg = "attempt to get gap columns with gap_ratio of unaligned msa"
433 raise StandardError, error_msg, caller
435 if ( gap_ratio < 0 || gap_ratio > 1 )
436 error_msg = "gap ratio must be between 0 and 1 inclusive"
437 raise ArgumentError, error_msg, caller
440 for c in 0 ... get_length
442 for s in 0 ... get_number_of_seqs
443 if Util.is_aa_gap_character?( get_sequence( s ).get_character_code( c ) )
447 if ( ( gap_chars_found.to_f / get_number_of_seqs ) > gap_ratio )
455 # Split an alignment into n alignemnts of equal size, except last one
456 def split( n, verbose = false )
457 if ( n < 2 || n > get_number_of_seqs )
458 error_msg = "attempt to split into less than two or more than the number of sequences"
459 raise StandardError, error_msg, caller
462 r = get_number_of_seqs % n
463 x = get_number_of_seqs / n
468 if ( ( r > 0 ) && ( i == ( n - 1 ) ) )
471 puts( i.to_s + ": " + y.to_s )
474 msa.add_sequence( get_sequence( ( i * x ) + j ) )
478 puts( i.to_s + ": " + x.to_s )
481 msa.add_sequence( get_sequence( ( i * x ) + j ) )
492 def get_overlaps( min_overlap = 1 )
494 error_msg = "attempt to get overlaps of unaligned msa"
495 raise StandardError, error_msg, caller
498 for i in 0 ... get_number_of_seqs()
500 for j in 0 ... bins.length
501 current_bin = bins[ j ]
502 # does seq i overlap with all seqs in current_bin?
504 for z in 0 ... current_bin.length
505 unless overlap?( i, current_bin[ z ], min_overlap )
511 current_bin.push( i )
516 new_bin = Array.new()
524 def remove_columns!( cols )
526 error_msg = "attempt to remove columns of unaligned msa"
527 raise StandardError, error_msg, caller
530 for c in 0 ... cols.length()
532 for s in 0 ... get_number_of_seqs()
533 get_sequence( s ).delete_residue!( col )