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()
176 for i in 0...get_number_of_seqs
177 s += @sequences[ i ].to_fasta + Constants::LINE_DELIMITER
183 def print_overlap_diagram( min_overlap = 1, io = STDOUT, max_name_length = 10 )
185 error_msg = "attempt to get overlap diagram of unaligned msa"
186 raise StandardError, error_msg, caller
188 for i in 0 ... get_number_of_seqs()
189 io.print( Util.normalize_seq_name( get_sequence( i ).get_name(), max_name_length ) )
190 for j in 0 ... get_number_of_seqs()
194 if overlap?( i, j, min_overlap )
201 io.print( Evoruby::Constants::LINE_DELIMITER )
205 #returns array of Msa with an overlap of min_overlap
206 def split_into_overlapping_msa( min_overlap = 1 )
208 error_msg = "attempt to split into overlapping msas of unaligned msa"
209 raise StandardError, error_msg, caller
212 bins = get_overlaps( min_overlap )
213 for i in 0 ... bins.length
214 msas.push( get_sub_alignment( bins[ i ] ) )
219 def overlap?( index_1, index_2, min_overlap = 1 )
220 seq_1 = get_sequence( index_1 )
221 seq_2 = get_sequence( index_2 )
223 for i in 0...seq_1.get_length()
224 if !Util.is_aa_gap_character?( seq_1.get_character_code( i ) ) &&
225 !Util.is_aa_gap_character?( seq_2.get_character_code( i ) )
227 if overlap_count >= min_overlap
235 def calculate_overlap( index_1, index_2 )
236 seq_1 = get_sequence( index_1 )
237 seq_2 = get_sequence( index_2 )
239 for i in 0...seq_1.get_length
240 if !Util.is_aa_gap_character?( seq_1.get_character_code( i ) ) &&
241 !Util.is_aa_gap_character?( seq_2.get_character_code( i ) )
248 def calculate_identities( index_1, index_2 )
249 seq_1 = get_sequence( index_1 )
250 seq_2 = get_sequence( index_2 )
252 for i in 0...seq_1.get_length
253 if !Util.is_aa_gap_character?( seq_1.get_character_code( i ) ) &&
254 !Util.is_aa_gap_character?( seq_2.get_character_code( i ) ) &&
255 seq_1.get_character_code( i ) != 63 &&
256 ( seq_1.get_residue( i ).downcase() ==
257 seq_2.get_residue( i ).downcase() )
258 identities_count += 1
264 def remove_gap_only_columns!()
265 remove_columns!( get_gap_only_columns() )
268 def remove_gap_columns!()
269 remove_columns!( get_gap_columns() )
272 # removes columns for which seqs with gap / number of sequences > gap_ratio
273 def remove_gap_columns_w_gap_ratio!( gap_ratio )
274 remove_columns!( get_gap_columns_w_gap_ratio( gap_ratio ) )
278 def remove_sequences_by_gap_ratio!( gap_ratio )
280 error_msg = "attempt to remove sequences by gap ratio on unaligned msa"
281 raise StandardError, error_msg, caller
283 n = get_number_of_seqs
286 if ( get_sequence( ( n - 1 ) - s ).get_gap_ratio() > gap_ratio )
287 if ( Evoruby::Constants::VERBOSE )
288 puts( "removed: " + get_sequence( ( n - 1 ) - s ).get_name )
290 removed << get_sequence( ( n - 1 ) - s ).get_name
291 remove_sequence!( ( n - 1 ) - s )
298 def remove_redundant_sequences!( consider_taxonomy = false, verbose = false )
299 n = get_number_of_seqs
301 to_be_removed = Set.new
302 @identical_seqs_detected = Array.new
303 for i in 0 ... ( n - 1 )
304 for j in ( i + 1 ) ... n
305 if !to_be_removed.include?( i ) && !to_be_removed.include?( j )
306 if !consider_taxonomy ||
307 ( ( get_sequence( i ).get_taxonomy == nil && get_sequence( j ).get_taxonomy == nil ) ||
308 ( get_sequence( i ).get_taxonomy == get_sequence( j ).get_taxonomy ) )
309 if Util.clean_seq_str( get_sequence( i ).get_sequence_as_string ) ==
310 Util.clean_seq_str( get_sequence( j ).get_sequence_as_string )
311 to_be_removed.add( j )
315 if get_sequence( i ).get_taxonomy != nil
316 tax_i = get_sequence( i ).get_taxonomy.get_name
318 if get_sequence( j ).get_taxonomy != nil
319 tax_j = get_sequence( j ).get_taxonomy.get_name
321 identical_pair = get_sequence( i ).get_name + " [#{tax_i}] == " + get_sequence( j ).get_name + " [#{tax_j}]"
322 @identical_seqs_detected.push( identical_pair )
332 to_be_removed_ary = to_be_removed.to_a.sort.reverse
334 to_be_removed_ary.each { | index |
335 removed.push( get_sequence( index ).get_name )
336 remove_sequence!( index )
342 def remove_sequences_by_non_gap_length!( min_non_gap_length )
344 error_msg = "attempt to remove sequences by non gap length on unaligned msa"
345 raise StandardError, error_msg, caller
347 n = get_number_of_seqs
351 if ( ( l - get_sequence( ( n - 1 ) - s ).get_gap_length ) < min_non_gap_length )
352 if ( Evoruby::Constants::VERBOSE )
353 puts( "removed: " + get_sequence( ( n - 1 ) - s ).get_name )
355 removed << get_sequence( ( n - 1 ) - s ).get_name
356 remove_sequence!( ( n - 1 ) - s )
362 def trim!( first, last )
364 for i in 0 ... get_length()
365 if ( i < first || i > last )
369 remove_columns!( cols )
372 def get_gap_only_columns()
374 error_msg = "attempt to get gap only columns of unaligned msa"
375 raise StandardError, error_msg, caller
378 for c in 0 ... get_length
379 nogap_char_found = false
380 for s in 0 ... get_number_of_seqs
381 unless Util.is_aa_gap_character?( get_sequence( s ).get_character_code( c ) )
382 nogap_char_found = true
386 unless nogap_char_found
393 def calculate_gap_proportion()
395 error_msg = "attempt to get gap only columns of unaligned msa"
396 raise StandardError, error_msg, caller
400 for c in 0 ... get_length
401 for s in 0 ... get_number_of_seqs
402 total_sum = total_sum + 1
403 if Util.is_aa_gap_character?( get_sequence( s ).get_character_code( c ) )
404 gap_sum = gap_sum + 1
409 return gap_sum / total_sum
412 def get_gap_columns()
414 error_msg = "attempt to get gap columns of unaligned msa"
415 raise StandardError, error_msg, caller
418 for c in 0 ... get_length
419 gap_char_found = false
420 for s in 0 ... get_number_of_seqs
421 if Util.is_aa_gap_character?( get_sequence( s ).get_character_code( c ) )
422 gap_char_found = true
433 # gap_ratio = seqs with gap / number of sequences
434 # returns column indices for which seqs with gap / number of sequences > gap_ratio
435 def get_gap_columns_w_gap_ratio( gap_ratio )
437 error_msg = "attempt to get gap columns with gap_ratio of unaligned msa"
438 raise StandardError, error_msg, caller
440 if ( gap_ratio < 0 || gap_ratio > 1 )
441 error_msg = "gap ratio must be between 0 and 1 inclusive"
442 raise ArgumentError, error_msg, caller
445 for c in 0 ... get_length
447 for s in 0 ... get_number_of_seqs
448 if Util.is_aa_gap_character?( get_sequence( s ).get_character_code( c ) )
452 if ( ( gap_chars_found.to_f / get_number_of_seqs ) > gap_ratio )
460 # Split an alignment into n alignemnts of equal size, except last one
461 def split( n, verbose = false )
462 if ( n < 2 || n > get_number_of_seqs )
463 error_msg = "attempt to split into less than two or more than the number of sequences"
464 raise StandardError, error_msg, caller
467 r = get_number_of_seqs % n
468 x = get_number_of_seqs / n
473 if ( ( r > 0 ) && ( i == ( n - 1 ) ) )
476 puts( i.to_s + ": " + y.to_s )
479 msa.add_sequence( get_sequence( ( i * x ) + j ) )
483 puts( i.to_s + ": " + x.to_s )
486 msa.add_sequence( get_sequence( ( i * x ) + j ) )
497 def get_overlaps( min_overlap = 1 )
499 error_msg = "attempt to get overlaps of unaligned msa"
500 raise StandardError, error_msg, caller
503 for i in 0 ... get_number_of_seqs()
505 for j in 0 ... bins.length
506 current_bin = bins[ j ]
507 # does seq i overlap with all seqs in current_bin?
509 for z in 0 ... current_bin.length
510 unless overlap?( i, current_bin[ z ], min_overlap )
516 current_bin.push( i )
521 new_bin = Array.new()
529 def remove_columns!( cols )
531 error_msg = "attempt to remove columns of unaligned msa"
532 raise StandardError, error_msg, caller
535 for c in 0 ... cols.length()
537 for s in 0 ... get_number_of_seqs()
538 get_sequence( s ).delete_residue!( col )