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comparison Roary/lib/Bio/Roary/SplitGroups.pm @ 0:c47a5f61bc9f draft

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author dereeper
date Fri, 14 May 2021 20:27:06 +0000
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1 package Bio::Roary::SplitGroups;
2
3 # ABSTRACT: split groups
4
5 =head1 SYNOPSIS
6
7 use Bio::Roary::SplitGroups;
8
9 =cut
10
11 use Moose;
12 use Bio::Roary::AnalyseGroups;
13 use File::Path qw(make_path remove_tree);
14 use File::Copy qw(move);
15 use File::Temp;
16 use File::Basename;
17 use File::Slurper 'read_lines';
18 use Cwd;
19
20
21 has 'groupfile' => ( is => 'ro', isa => 'Str', required => 1 );
22 has 'fasta_files' => ( is => 'ro', isa => 'ArrayRef', required => 1 );
23 has 'outfile' => ( is => 'ro', isa => 'Str', required => 1 );
24 has 'iterations' => ( is => 'ro', isa => 'Int', default => 5 );
25 has 'dont_delete' => ( is => 'ro', isa => 'Bool', default => 0 );
26
27 has '_neighbourhood_size' => ( is => 'ro', isa => 'Int', default => 5 );
28
29 has '_group_filelist' => ( is => 'rw', isa => 'ArrayRef', lazy_build => 1 );
30 has '_tmp_dir_object' => ( is => 'ro', isa => 'File::Temp::Dir', default => sub { File::Temp->newdir( DIR => getcwd, CLEANUP => 1 ); } );
31 has '_tmp_dir' => ( is => 'ro', isa => 'Str', lazy => 1, builder => '_build__tmp_dir' );
32
33 has '_analyse_groups_obj' => ( is => 'ro', lazy_build => 1 );
34 has '_genes_to_files' => ( is => 'ro', lazy_build => 1 );
35 has '_genes_to_groups' => ( is => 'rw', isa => 'HashRef' );
36
37 has '_first_gene_of_group_which_doesnt_have_paralogs' => ( is => 'rw', isa => 'HashRef', default => sub {{}} );
38
39 has '_genes_to_neighbourhood' => ( is => 'rw', isa => 'HashRef', lazy => 1, builder => '_build__genes_to_neighbourhood' );
40
41
42 has '_gene_files_temp_dir_obj' =>
43 ( is => 'ro', isa => 'File::Temp::Dir', default => sub { File::Temp->newdir( DIR => getcwd, CLEANUP => 1 ); } );
44
45
46 has '_do_sorting' => ( is => 'rw', isa => 'Bool', default => 0 ); # set to 1 for testing only
47
48 sub _build__tmp_dir {
49 my ($self) = @_;
50 return $self->_tmp_dir_object->dirname();
51 }
52
53 sub _build__analyse_groups_obj {
54 my ( $self ) = @_;
55
56 return Bio::Roary::AnalyseGroups->new(
57 fasta_files => $self->fasta_files,
58 groups_filename => $self->groupfile
59 );
60 }
61
62 sub _build__genes_to_files {
63 my ( $self ) = @_;
64 return $self->_analyse_groups_obj->_genes_to_file;
65 }
66
67 sub _build__group_filelist {
68 my ( $self ) = @_;
69 my $tmp = $self->_tmp_dir;
70
71 my @filelist = ( $self->groupfile );
72 for my $i ( 1..($self->iterations - 1) ){
73 push( @filelist, "$tmp/group_$i" );
74 }
75 push( @filelist, $self->outfile );
76
77 return \@filelist;
78 }
79
80 sub _build__genes_to_neighbourhood
81 {
82 my ( $self ) = @_;
83 my %genes_to_neighbourhood;
84 for my $fasta_file( @{$self->fasta_files})
85 {
86 my ( $filename, $directories, $suffix ) = fileparse( $fasta_file, qr/\.[^.]*/ );
87 system('grep \> '.$fasta_file.'| sed \'s/>//\' >'.$self->_gene_files_temp_dir_obj."/".$filename.$suffix ) ;
88
89 my @genes = read_lines($self->_gene_files_temp_dir_obj."/".$filename.$suffix );
90
91 for(my $i =0; $i< @genes; $i++)
92 {
93 for(my $offset = 1; $offset <= $self->_neighbourhood_size; $offset++)
94 {
95 if($i -$offset >= 0)
96 {
97 push(@{$genes_to_neighbourhood{$genes[$i]}}, $genes[$i - $offset ]);
98 }
99 if($i +$offset <@genes)
100 {
101 push(@{$genes_to_neighbourhood{$genes[$i]}}, $genes[$i + $offset ]);
102 }
103 }
104 }
105 }
106 return \%genes_to_neighbourhood;
107 }
108
109 sub split_groups {
110 my ( $self ) = @_;
111
112 # iteratively
113 for my $x ( 0..($self->iterations - 1) ){
114 my ( $in_groups, $out_groups ) = $self->_get_files_for_iteration( $x );
115
116 # read in groups, check paralogs and split
117 my @newgroups;
118 my $any_paralogs = 0;
119 $self->_set_genes_to_groups( $in_groups );
120 open( my $group_handle, '<', $in_groups );
121 while( my $line = <$group_handle> ){
122 my @group = split( /\s+/, $line );
123
124 if($self->_first_gene_of_group_which_doesnt_have_paralogs->{$group[0]})
125 {
126 push( @newgroups, \@group );
127 }
128 elsif(@group == 1)
129 {
130 $self->_first_gene_of_group_which_doesnt_have_paralogs->{$group[0]}++;
131 push( @newgroups, \@group );
132 }
133 elsif( $self->_contains_paralogs( \@group ) ){
134 my @true_orthologs = @{ $self->_true_orthologs( \@group ) };
135 push( @newgroups, @true_orthologs);
136 $any_paralogs = 1;
137 }
138 else {
139 $self->_first_gene_of_group_which_doesnt_have_paralogs->{$group[0]}++;
140 push( @newgroups, \@group );
141 }
142 }
143 close( $group_handle );
144
145 # check if next iteration required, move output if not
146 unless ($any_paralogs){
147 move $in_groups, $self->outfile; # input file will be the same as new output file if no splitting has been performed
148 last;
149 }
150
151 # write split groups to file
152 open( my $outfile_handle, '>', $out_groups );
153 for my $g ( @newgroups ) {
154 my $group_str = join( "\t", @{ $g } ) . "\n";
155 print $outfile_handle $group_str;
156 }
157 close( $outfile_handle );
158 }
159 }
160
161 sub _set_genes_to_groups {
162 my ( $self, $groupfile ) = @_;
163
164 my %genes2groups;
165 my $c = 0;
166 open( my $gfh, '<', $groupfile );
167 while( my $line = <$gfh> ){
168 chomp $line;
169 my @genes = split( /\s+/, $line );
170 for my $g ( @genes ){
171 $genes2groups{$g} = $c;
172 }
173 $c++;
174 }
175 close($gfh);
176 $self->_genes_to_groups( \%genes2groups );
177 }
178
179 sub _update_genes_to_groups {
180 my ( $self, $groups ) = @_;
181
182 my %genes2groups = %{ $self->_genes_to_groups };
183 my $c = 1;
184 for my $g ( @{ $groups } ){
185 for my $h ( @{ $g } ){
186 $genes2groups{$h} .= ".$c";
187 }
188 $c++;
189 }
190
191 $self->_genes_to_groups( \%genes2groups );
192 }
193
194 sub _get_files_for_iteration {
195 my ( $self, $n ) = @_;
196 my @filelist = @{ $self->_group_filelist };
197 return ( $filelist[$n], $filelist[$n+1] );
198 }
199
200 sub _contains_paralogs {
201 my ( $self, $group ) = @_;
202
203 return 1 if defined $self->_find_paralogs( $group );
204 return 0;
205 }
206
207 sub _find_paralogs {
208 my ( $self, $group ) = @_;
209
210 my %occ;
211 for my $gene ( @{ $group } ){
212 my $gene_file = $self->_genes_to_files->{ $gene };
213 push( @{ $occ{$gene_file} }, $gene );
214 }
215
216 # pick the smallest number of paralogs
217 my $smallest_number = 1000000;
218 my $smallest_group;
219 for my $v ( values %occ ){
220 my $v_len = scalar( @{$v} );
221 if ( $v_len < $smallest_number && $v_len > 1 ){
222 $smallest_number = $v_len;
223 $smallest_group = $v;
224 }
225 }
226 return $smallest_group if ( defined $smallest_group );
227
228 return undef;
229 }
230
231 sub _true_orthologs {
232 my ( $self, $group ) = @_;
233
234 # first, create CGN hash for group
235 my %cgns;
236 for my $g ( @{ $group } ){
237 $cgns{$g} = $self->_parse_gene_neighbourhood( $g );
238 }
239
240 # finding paralogs in the group
241 my @paralogs = @{ $self->_find_paralogs( $group ) };
242 my @paralog_cgns_groups;
243 for my $p ( @paralogs ){
244 my %paralog_groups ;
245 for my $paralog_gene (@{$cgns{$p}})
246 {
247 my $gene_paralog_group = $self->_genes_to_groups->{$paralog_gene};
248 next unless( defined($gene_paralog_group));
249 $paralog_groups{$self->_genes_to_groups->{$paralog_gene}}++;
250 }
251 push( @paralog_cgns_groups, \%paralog_groups );
252 }
253
254 # create data structure to hold new groups
255 my @new_groups;
256 for my $p ( @paralogs ){
257 push( @new_groups, [ $p ] );
258 }
259 push( @new_groups, [] ); # extra "leftovers" array to gather genes that don't share CGN with anything
260
261 # cluster other members of the group to their closest match
262 for my $g ( @{ $group } ){
263 next if ( grep {$_ eq $g} @paralogs );
264 my $closest = $self->_closest_cgn( $cgns{$g}, \@paralog_cgns_groups );
265 push( @{ $new_groups[$closest] }, $g );
266 }
267
268 # check for "leftovers", remove if absent
269 my $last = pop @new_groups;
270 push( @new_groups, $last ) if ( @$last > 0 );
271
272 # sort
273 if ( $self->_do_sorting ){
274 my @sorted_new_groups;
275 for my $gr ( @new_groups ){
276 my @s_gr = sort @{ $gr };
277 push( @sorted_new_groups, \@s_gr );
278 }
279 return \@sorted_new_groups;
280 }
281
282 return \@new_groups;
283 }
284
285 sub _closest_cgn {
286 my ( $self, $cgn, $p_cgns ) = @_;
287
288 my @paralog_cgns = @{ $p_cgns };
289 my $best_score = 0;
290 my $bs_index = -1; # return -1 to add to "leftovers" array if no better score is found
291 for my $i ( 0..$#paralog_cgns ){
292 my $p_cgn = $paralog_cgns[$i];
293 my $score = $self->_shared_cgn_score( $cgn, $p_cgn );
294 if ( $score > $best_score ){
295 $best_score = $score;
296 $bs_index = $i;
297 }
298 }
299 return $bs_index;
300 }
301
302 sub _shared_cgn_score {
303 my ( $self, $cgn1, $cgn2 ) = @_;
304
305 my $total_shared = 0;
306 for my $i ( @{ $cgn1 } ){
307 my $input_group = $self->_genes_to_groups->{$i};
308 next unless(defined($input_group));
309 $total_shared++ if($cgn2->{$input_group});
310 }
311 if( (scalar @{ $cgn1 }) == 0)
312 {
313 return 0;
314 }
315 my $score = $total_shared/scalar @{ $cgn1 };
316 return $score;
317 }
318
319 sub _parse_gene_neighbourhood {
320 my ( $self, $gene_id ) = @_;
321
322 return $self->_genes_to_neighbourhood->{$gene_id };
323
324 }
325
326 no Moose;
327 __PACKAGE__->meta->make_immutable;
328 1;