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Revision 1.3 - (view) (download)

1 : redwards 1.1
2 :     =pod
3 :    
4 :     =head1
5 :    
6 :     Create a summary of subsystems
7 :    
8 :     =cut
9 :    
10 :     use strict;
11 :     use FIG;
12 :     use HTML;
13 :     use raelib;
14 :     use CGI;
15 :     my $cgi=new CGI;
16 :    
17 :    
18 :     my $fig;
19 :     eval {
20 :     $fig = new FIG;
21 :     };
22 :    
23 :     if ($@ ne "")
24 :     {
25 :     my $err = $@;
26 :    
27 :     my(@html);
28 :    
29 :     push(@html, $cgi->p("Error connecting to SEED database."));
30 :     if ($err =~ /Could not connect to DBI:.*could not connect to server/)
31 :     {
32 :     push(@html, $cgi->p("Could not connect to relational database of type $FIG_Config::dbms named $FIG_Config::db on port $FIG_Config::dbport."));
33 :     }
34 :     else
35 :     {
36 :     push(@html, $cgi->pre($err));
37 :     }
38 :     &HTML::show_page($cgi, \@html, 1);
39 :     exit;
40 :     }
41 :    
42 :    
43 :    
44 :     $ENV{"PATH"} = "$FIG_Config::bin:$FIG_Config::ext_bin:" . $ENV{"PATH"};
45 :    
46 :     my $html = [];
47 :    
48 :    
49 :     if ($cgi->param('submit') eq "Summarize Subsystems")
50 :     {
51 :     summarize_ss();
52 :     }
53 :     else
54 :     {
55 :     show_initial();
56 :     }
57 :    
58 :     unshift @$html, "<TITLE>The SEED - Subsystem summarizer </TITLE>\n";
59 :     &HTML::show_page($cgi, $html, 1);
60 :     exit;
61 :    
62 :    
63 :    
64 :    
65 :    
66 :    
67 :    
68 :    
69 :    
70 :    
71 :     sub summarize_ss {
72 :     my @wants;
73 :     foreach my $w ($cgi->param('korgs')) {
74 :     $w =~ /\((\d+\.\d+)\)/;
75 :     push @wants, $1;
76 :     }
77 :    
78 :    
79 :     my @th;
80 : redwards 1.2 if ($cgi->param('levels')) {push @th, ('Level 1', 'Level 2')}
81 :     push @th, 'Subsystem'; # we should have this, at least
82 :     if ($cgi->param('genomes')) {push @th, ('Organisms')}
83 :     if ($cgi->param('stats')) {push @th, ('Roles', 'Total Pegs', @wants)}
84 : redwards 1.3 elsif ($cgi->param('korgs')) {push @th, ('Roles', @wants)}
85 : redwards 1.1
86 :     my $tableheader="<tr><th>". (join "</th><th>", @th) . "</th></tr>\n\n";
87 :    
88 :     my $cols=scalar @th;
89 :     my $table;
90 :     foreach my $subsys ($fig->all_subsystems) {
91 :    
92 :     # figure out how many roles we have, as this will determine the number of rows in the table
93 :     my @roles=$fig->subsystem_to_roles($subsys);
94 :     my $rows=1;
95 : redwards 1.3 if (!$cgi->param('stats') && $cgi->param('korgs')) {$rows=scalar @roles}
96 : redwards 1.1
97 :     # figure out which genomes are in this subsystem
98 :     my %genomes;
99 :     foreach my $gen (@{$fig->subsystem_genomes($subsys)}) {$genomes{$gen->[0]}=$gen->[1]}
100 :    
101 : redwards 1.2 # start a new row for this data
102 : redwards 1.3 # tablerows is a refence to an array.
103 :     # each element is an array of tablecells with the following values colspan rowspan value
104 :     my $tablerows;
105 : redwards 1.2
106 : redwards 1.1 # get the classification if required
107 :     if ($cgi->param('levels')) {
108 : redwards 1.2 # get the classification and make sure there are now 2 columns as andrei doesn't like #3.
109 : redwards 1.1 my $class=$fig->subsystem_classification($subsys);
110 : redwards 1.2 unless ($class) {@$class=(' &nbsp; ',' &nbsp; ')}
111 :     unless ($$class[0]) {$$class[0] = " &nbsp; "}
112 :     unless ($$class[1]) {$$class[1] = " &nbsp; "}
113 :     # remove anything more than $$class[1];
114 :     @$class=($$class[0], $$class[1]); # could have done this with splice. Ech.
115 :    
116 : redwards 1.3 foreach my $c (@$class) {
117 :     push @$tablerows, ['1', $rows, $c];
118 :     }
119 : redwards 1.1 }
120 :    
121 : redwards 1.2 # add the subsystem to the table
122 : redwards 1.3 push @$tablerows, ['1', $rows, "<strong>$subsys<strong>"];
123 : redwards 1.2
124 : redwards 1.1 # add the genomes in the subsystem
125 : redwards 1.3 if ($cgi->param('genomes') && $cgi->param('stats')) {push @$tablerows, ['1', $rows, (scalar keys %genomes)]}
126 :     elsif ($cgi->param('genomes')) {
127 :     my $c=join "<br>\n", sort {$a cmp $b} values %genomes;
128 :     push @$tablerows, ['1', $rows, $c];
129 :     }
130 : redwards 1.2
131 : redwards 1.3
132 :     #
133 :     # This is convolvuted because we may want to skip some empty cells, but we won't know whether
134 :     # we want to skip them. Also, we are using rowspan/colspan to determine the size of the cells
135 :     # so we need everything defined
136 :     #
137 :     # I store the table initially in @$tablerows, and then push it into @$table. Later on we
138 :     # reconstruct @$table with <td> etc....
139 :     #
140 :     # Now I am going to store the rows in @$toadd, and if we want them I will add them to @$table.
141 :     #
142 :     # For stats, there is only one row in @$toadd, but for other data there are several because
143 :     # of the use of rowspan
144 :    
145 :     my $pegcount;
146 :     my $toadd; #this is what we will add if we need to
147 : redwards 1.2 if ($cgi->param('stats')) {
148 : redwards 1.3 push @$tablerows, ['1', $rows, (scalar @roles)];
149 :     my $totalpegs;
150 : redwards 1.2 # there should be a quicker way of getting this ... ?
151 :     foreach my $role (@roles) {
152 :     foreach my $genome (keys %genomes) {
153 :     my $count = scalar ($fig->pegs_in_subsystem_cell($subsys, $genome, $role));
154 :     $pegcount->{$genome} += $count;
155 :     $totalpegs += $count;
156 :     }
157 :     }
158 : redwards 1.3
159 :     push @$tablerows, ['1', $rows, $totalpegs];
160 : redwards 1.2 foreach my $w (@wants) {
161 : redwards 1.3 push @$tablerows, ['1', $rows, $pegcount->{$w}]; # pegs for each of the chosen genomes
162 : redwards 1.2 }
163 : redwards 1.3 push @$toadd, $tablerows;
164 : redwards 1.2 }
165 : redwards 1.3 elsif ($cgi->param('korgs')) {
166 : redwards 1.1 # now add the roles
167 :     my $first=1;
168 :     foreach my $role (@roles) {
169 :     my $genomeroles;
170 :     foreach my $gen (@wants) {
171 : redwards 1.2 my $cell = ' &nbsp; ';
172 : redwards 1.1 if ($genomes{$gen}) {
173 :     foreach my $peg ($fig->pegs_in_subsystem_cell($subsys, $gen, $role)) {
174 :     $cell .= &HTML::fid_link($cgi,$peg) . "; ";
175 :     }
176 :     }
177 : redwards 1.3 push @$genomeroles, [1, 1, $cell];
178 : redwards 1.1 }
179 :     # because I am using rowspan to make long columns, we don't want the tr on the first of these.
180 : redwards 1.3 if ($first) {
181 :     push @$tablerows, (['1', '1', $role], @$genomeroles);
182 :     push @$toadd, $tablerows;
183 :     }
184 :     else {
185 :     my $tr=[('1', '1', $role), @$genomeroles];
186 :     push @$toadd, $tr;
187 :     }
188 : redwards 1.1 }
189 :     }
190 : redwards 1.3 unless ($toadd) {$toadd=$tablerows} # in case we didn't define it
191 :     # now decide if we want the table
192 :     if ($cgi->param('orgpegs')) {
193 :     my $mustadd;
194 :     foreach my $org (@wants) {if ($pegcount->{$org}) {$mustadd=1}} # we'll add it if one of the orgs has a role
195 :     if ($mustadd) {push @$table, @$toadd}
196 :     }
197 :     elsif ($cgi->param("haveroles")) {
198 :     if (scalar(@roles)) {push @$table, @$toadd}
199 :     }
200 :     else {
201 :     push @$table, @$toadd;
202 :     }
203 :     }
204 :    
205 :     # now convert $table into a table
206 :    
207 :     my $tab;
208 :     foreach my $row (@$table) {
209 :     $tab .= "\n<tr>";
210 :     foreach my $cell (@$row) {
211 :     $tab .= "\n\t<td colspan=$cell->[0] rowspan=$cell->[1]>$cell->[2]</td>";
212 :     }
213 :     $tab .= "\n</tr>\n";
214 : redwards 1.1 }
215 : redwards 1.3
216 :     push @$html, ("\n<table border=1>" . $tableheader . $tab . "</table>\n");
217 : redwards 1.1 }
218 :    
219 :    
220 :    
221 :    
222 :    
223 :    
224 :    
225 :    
226 :    
227 :    
228 :     sub show_initial {
229 :     #############
230 :     #
231 :     # Stolen from index.cgi
232 :     #
233 :     #
234 :    
235 :     my @display = ( 'All', 'Archaea', 'Bacteria', 'Eucarya', 'Viruses', 'Environmental samples' );
236 :    
237 :     #
238 :     # Canonical names must match the keywords used in the DBMS. They are
239 :     # defined in compute_genome_counts.pl
240 :     #
241 :     my %canonical = (
242 :     'All' => undef,
243 :     'Archaea' => 'Archaea',
244 :     'Bacteria' => 'Bacteria',
245 :     'Eucarya' => 'Eukaryota',
246 :     'Viruses' => 'Virus',
247 :     'Environmental samples' => 'Environmental Sample'
248 :     );
249 :    
250 :     my $req_dom = $cgi->param( 'domain' ) || 'All';
251 :     my @domains = $cgi->radio_group( -name => 'domain',
252 :     -default => $req_dom,
253 :     -override => 1,
254 :     -values => [ @display ]
255 :     );
256 :    
257 :     my $n_domain = 0;
258 :     my %dom_num = map { ( $_, $n_domain++ ) } @display;
259 :     my $req_dom_num = $dom_num{ $req_dom } || 0;
260 :    
261 :     #
262 :     # Viruses and Environmental samples must have completeness = All (that is
263 :     # how they are in the database). Otherwise, default is Only "complete".
264 :     #
265 :     my $req_comp = ( $req_dom_num > $dom_num{ 'Eucarya' } ) ? 'All'
266 :     : $cgi->param( 'complete' ) || 'Only "complete"';
267 :     my @complete = $cgi->radio_group( -name => 'complete',
268 :     -default => $req_comp,
269 :     -override => 1,
270 :     -values => [ 'All', 'Only "complete"' ]
271 :     );
272 :     #
273 :     # Use $fig->genomes( complete, restricted, domain ) to get org list:
274 :     #
275 :     my $complete = ( $req_comp =~ /^all$/i ) ? undef : "complete";
276 :    
277 :     my @orgs = sort map { my $org = $_; my $gs = $fig->genus_species($org); my $gc=scalar $fig->all_contigs($org); "$gs ($org) [$gc contigs]" }
278 :     $fig->genomes( $complete, undef, $canonical{ $req_dom } );
279 :    
280 :     my $n_genomes = @orgs;
281 :    
282 :     push @$html, $cgi->start_form,
283 :     $cgi->h2("Please choose one or more organisms from the list below to see in the subsystems table"),
284 :     "<TABLE>\n",
285 :     " <TR>\n",
286 :     " <TD>",
287 :     $cgi->scrolling_list( -name => 'korgs',
288 :     -size => 10,
289 :     -multiple => 1,
290 :     -values => \@orgs,
291 :     ),
292 :     $cgi->br,
293 :     "$n_genomes genomes shown ",
294 :     $cgi->submit( 'Update List' ), $cgi->reset, $cgi->submit('submit', 'Summarize Subsystems'),
295 :     "</TD>",
296 :     " <TD>",
297 :     join( "<br>", "<b>Domain(s) to show:</b>", @domains), "<br>\n",
298 :     join( "<br>", "<b>Completeness?</b>", @complete), "\n",
299 :     "</TD>",
300 :     " </TR>\n",
301 :     "</TABLE>\n",
302 :     $cgi->p,
303 : redwards 1.2 $cgi->checkbox(-name=>"stats", -label=>"Only show statistics", -checked=>'on'), $cgi->p,
304 : redwards 1.1 $cgi->checkbox(-name=>"levels", -label=>"Show subsystem classification", -checked=>'on'), $cgi->p,
305 :     $cgi->checkbox(-name=>"genomes", -label=>"Show genomes in subsystem", -checked=>'on'), $cgi->p,
306 : redwards 1.3 $cgi->checkbox(-name=>"haveroles", -label=>"Show only subsystems that have roles defined", -checked=>'on'), $cgi->p,
307 :     $cgi->checkbox(-name=>"orgpegs", -label=>"Show only subsystems that have roles in the organism(s) you have chosen", -checked=>'on'), $cgi->p,
308 :    
309 : redwards 1.1 $cgi->end_form,
310 :    
311 :     }
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