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Revision 1.8 - (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 : redwards 1.5 my @wantheaders;
80 :     foreach my $gen (@wants) {push @wantheaders, $fig->abbrev($fig->genus_species($gen))}
81 :    
82 : redwards 1.1 my @th;
83 : redwards 1.2 if ($cgi->param('levels')) {push @th, ('Level 1', 'Level 2')}
84 :     push @th, 'Subsystem'; # we should have this, at least
85 :     if ($cgi->param('genomes')) {push @th, ('Organisms')}
86 : redwards 1.5 if ($cgi->param('stats')) {push @th, ('Roles', 'Total Pegs', @wantheaders)}
87 :     elsif ($cgi->param('korgs')) {push @th, ('Roles', @wantheaders)}
88 : redwards 1.1
89 :     my $tableheader="<tr><th>". (join "</th><th>", @th) . "</th></tr>\n\n";
90 :    
91 :     my $cols=scalar @th;
92 :     my $table;
93 :     foreach my $subsys ($fig->all_subsystems) {
94 :    
95 :     # figure out how many roles we have, as this will determine the number of rows in the table
96 :     my @roles=$fig->subsystem_to_roles($subsys);
97 :     my $rows=1;
98 : redwards 1.3 if (!$cgi->param('stats') && $cgi->param('korgs')) {$rows=scalar @roles}
99 : redwards 1.1
100 :     # figure out which genomes are in this subsystem
101 :     my %genomes;
102 :     foreach my $gen (@{$fig->subsystem_genomes($subsys)}) {$genomes{$gen->[0]}=$gen->[1]}
103 :    
104 : redwards 1.2 # start a new row for this data
105 : redwards 1.3 # tablerows is a refence to an array.
106 : redwards 1.4 # each element is an array of tablecells with the following values value colspan rowspan width
107 :     # if colspan or rowspan are undef they are believed to be 1
108 :     # if width is ommitted it is ignored
109 :    
110 : redwards 1.3 my $tablerows;
111 : redwards 1.7 my $mt; #DELETE THIS
112 : redwards 1.1 # get the classification if required
113 :     if ($cgi->param('levels')) {
114 : redwards 1.2 # get the classification and make sure there are now 2 columns as andrei doesn't like #3.
115 : redwards 1.1 my $class=$fig->subsystem_classification($subsys);
116 : redwards 1.2 unless ($class) {@$class=(' &nbsp; ',' &nbsp; ')}
117 :     unless ($$class[0]) {$$class[0] = " &nbsp; "}
118 :     unless ($$class[1]) {$$class[1] = " &nbsp; "}
119 :     # remove anything more than $$class[1];
120 :     @$class=($$class[0], $$class[1]); # could have done this with splice. Ech.
121 :    
122 : redwards 1.3 foreach my $c (@$class) {
123 : redwards 1.5 push @$tablerows, [$c, 1, $rows, 20];
124 : redwards 1.3 }
125 : redwards 1.1 }
126 :    
127 : redwards 1.2 # add the subsystem to the table
128 : redwards 1.4 push @$tablerows, ["<strong>$subsys<strong>", '1', $rows];
129 : redwards 1.2
130 : redwards 1.1 # add the genomes in the subsystem
131 : redwards 1.4 if ($cgi->param('genomes') && $cgi->param('stats')) {push @$tablerows, [(scalar keys %genomes), '1', $rows]}
132 : redwards 1.3 elsif ($cgi->param('genomes')) {
133 :     my $c=join "<br>\n", sort {$a cmp $b} values %genomes;
134 : redwards 1.4 push @$tablerows, [$c, 1, $rows];
135 : redwards 1.3 }
136 : redwards 1.2
137 : redwards 1.3 #
138 :     # This is convolvuted because we may want to skip some empty cells, but we won't know whether
139 :     # we want to skip them. Also, we are using rowspan/colspan to determine the size of the cells
140 :     # so we need everything defined
141 :     #
142 :     # I store the table initially in @$tablerows, and then push it into @$table. Later on we
143 :     # reconstruct @$table with <td> etc....
144 :     #
145 :     # Now I am going to store the rows in @$toadd, and if we want them I will add them to @$table.
146 :     #
147 :     # For stats, there is only one row in @$toadd, but for other data there are several because
148 :     # of the use of rowspan
149 :    
150 :     my $pegcount;
151 :     my $toadd; #this is what we will add if we need to
152 : redwards 1.2 if ($cgi->param('stats')) {
153 : redwards 1.4 push @$tablerows, [(scalar @roles), '1', $rows];
154 : redwards 1.3 my $totalpegs;
155 : redwards 1.2 # there should be a quicker way of getting this ... ?
156 :     foreach my $role (@roles) {
157 :     foreach my $genome (keys %genomes) {
158 :     my $count = scalar ($fig->pegs_in_subsystem_cell($subsys, $genome, $role));
159 :     $pegcount->{$genome} += $count;
160 :     $totalpegs += $count;
161 :     }
162 :     }
163 : redwards 1.3
164 : redwards 1.4 push @$tablerows, [$totalpegs, '1', $rows];
165 : redwards 1.2 foreach my $w (@wants) {
166 : redwards 1.4 push @$tablerows, [$pegcount->{$w}, '1', $rows]; # pegs for each of the chosen genomes
167 : redwards 1.2 }
168 : redwards 1.3 push @$toadd, $tablerows;
169 : redwards 1.2 }
170 : redwards 1.3 elsif ($cgi->param('korgs')) {
171 : redwards 1.1 my $first=1;
172 :     foreach my $role (@roles) {
173 :     my $genomeroles;
174 :     foreach my $gen (@wants) {
175 : redwards 1.2 my $cell = ' &nbsp; ';
176 : redwards 1.1 if ($genomes{$gen}) {
177 :     foreach my $peg ($fig->pegs_in_subsystem_cell($subsys, $gen, $role)) {
178 : redwards 1.6 $cell .= &HTML::fid_link($cgi,$peg, 'local') . "; ";
179 : redwards 1.1 }
180 :     }
181 : redwards 1.4 push @$genomeroles, [$cell, 1, 1];
182 : redwards 1.1 }
183 :     # because I am using rowspan to make long columns, we don't want the tr on the first of these.
184 : redwards 1.3 if ($first) {
185 : redwards 1.7 push @$tablerows, [$role, 1, 1], @$genomeroles;
186 : redwards 1.8 push @$toadd, $tablerows;
187 : redwards 1.4 undef $first;
188 : redwards 1.3 }
189 :     else {
190 : redwards 1.4 my @tr=([$role, 1, 1], @$genomeroles);
191 : redwards 1.8 push @$toadd, \@tr;
192 : redwards 1.3 }
193 : redwards 1.1 }
194 :     }
195 : redwards 1.5
196 :     unless ($toadd) {
197 : redwards 1.8 push @$toadd, $tablerows;
198 : redwards 1.5 } # in case we didn't define it
199 :    
200 :    
201 : redwards 1.3 # now decide if we want the table
202 :     if ($cgi->param('orgpegs')) {
203 :     my $mustadd;
204 :     foreach my $org (@wants) {if ($pegcount->{$org}) {$mustadd=1}} # we'll add it if one of the orgs has a role
205 : redwards 1.8 if ($mustadd) {push @$table, @$toadd}
206 : redwards 1.3 }
207 :     elsif ($cgi->param("haveroles")) {
208 : redwards 1.8 if (scalar(@roles)) {push @$table, @$toadd}
209 : redwards 1.3 }
210 :     else {
211 : redwards 1.8 push @$table, @$toadd;
212 : redwards 1.3 }
213 :     }
214 :    
215 :     # now convert $table into a table
216 : redwards 1.4
217 :     # sort the table
218 :     # if we have levels we want to sort on level 1 and then level 2 and then subsysname
219 :     # if not, we just sort on subsys name
220 :     if ($cgi->param("levels")) {
221 :     @$table = sort {
222 :     $a->[0]->[0] cmp $b->[0]->[0]
223 :     ||
224 :     $a->[1]->[0] cmp $b->[1]->[0]
225 :     ||
226 :     $a->[2]->[0] cmp $b->[2]->[0]
227 :     } @$table;
228 :     }
229 :     else {
230 :     @$table = sort {
231 :     $a->[0]->[0] cmp $b->[0]->[0]
232 :     } @$table;
233 :     }
234 :    
235 :    
236 : redwards 1.3 my $tab;
237 :     foreach my $row (@$table) {
238 :     $tab .= "\n<tr>";
239 :     foreach my $cell (@$row) {
240 : redwards 1.5 my $width='';
241 : redwards 1.6 if ($cell->[3]) {$width="width=" . $cell->[3]}
242 : redwards 1.5 $tab .= "\n\t<td valign=top $width colspan=$cell->[1] rowspan=$cell->[2]>$cell->[0]</td>";
243 : redwards 1.3 }
244 :     $tab .= "\n</tr>\n";
245 : redwards 1.1 }
246 : redwards 1.3
247 :     push @$html, ("\n<table border=1>" . $tableheader . $tab . "</table>\n");
248 : redwards 1.1 }
249 :    
250 :    
251 :    
252 :    
253 :    
254 :    
255 :    
256 :    
257 :    
258 :    
259 :     sub show_initial {
260 :     #############
261 :     #
262 :     # Stolen from index.cgi
263 :     #
264 :     #
265 :    
266 :     my @display = ( 'All', 'Archaea', 'Bacteria', 'Eucarya', 'Viruses', 'Environmental samples' );
267 :    
268 :     #
269 :     # Canonical names must match the keywords used in the DBMS. They are
270 :     # defined in compute_genome_counts.pl
271 :     #
272 :     my %canonical = (
273 :     'All' => undef,
274 :     'Archaea' => 'Archaea',
275 :     'Bacteria' => 'Bacteria',
276 :     'Eucarya' => 'Eukaryota',
277 :     'Viruses' => 'Virus',
278 :     'Environmental samples' => 'Environmental Sample'
279 :     );
280 :    
281 :     my $req_dom = $cgi->param( 'domain' ) || 'All';
282 :     my @domains = $cgi->radio_group( -name => 'domain',
283 :     -default => $req_dom,
284 :     -override => 1,
285 :     -values => [ @display ]
286 :     );
287 :    
288 :     my $n_domain = 0;
289 :     my %dom_num = map { ( $_, $n_domain++ ) } @display;
290 :     my $req_dom_num = $dom_num{ $req_dom } || 0;
291 :    
292 :     #
293 :     # Viruses and Environmental samples must have completeness = All (that is
294 :     # how they are in the database). Otherwise, default is Only "complete".
295 :     #
296 :     my $req_comp = ( $req_dom_num > $dom_num{ 'Eucarya' } ) ? 'All'
297 :     : $cgi->param( 'complete' ) || 'Only "complete"';
298 :     my @complete = $cgi->radio_group( -name => 'complete',
299 :     -default => $req_comp,
300 :     -override => 1,
301 :     -values => [ 'All', 'Only "complete"' ]
302 :     );
303 :     #
304 :     # Use $fig->genomes( complete, restricted, domain ) to get org list:
305 :     #
306 :     my $complete = ( $req_comp =~ /^all$/i ) ? undef : "complete";
307 :    
308 :     my @orgs = sort map { my $org = $_; my $gs = $fig->genus_species($org); my $gc=scalar $fig->all_contigs($org); "$gs ($org) [$gc contigs]" }
309 :     $fig->genomes( $complete, undef, $canonical{ $req_dom } );
310 :    
311 :     my $n_genomes = @orgs;
312 :    
313 :     push @$html, $cgi->start_form,
314 :     $cgi->h2("Please choose one or more organisms from the list below to see in the subsystems table"),
315 :     "<TABLE>\n",
316 :     " <TR>\n",
317 :     " <TD>",
318 :     $cgi->scrolling_list( -name => 'korgs',
319 :     -size => 10,
320 :     -multiple => 1,
321 :     -values => \@orgs,
322 :     ),
323 :     $cgi->br,
324 :     "$n_genomes genomes shown ",
325 :     $cgi->submit( 'Update List' ), $cgi->reset, $cgi->submit('submit', 'Summarize Subsystems'),
326 :     "</TD>",
327 :     " <TD>",
328 :     join( "<br>", "<b>Domain(s) to show:</b>", @domains), "<br>\n",
329 :     join( "<br>", "<b>Completeness?</b>", @complete), "\n",
330 :     "</TD>",
331 :     " </TR>\n",
332 :     "</TABLE>\n",
333 :     $cgi->p,
334 : redwards 1.2 $cgi->checkbox(-name=>"stats", -label=>"Only show statistics", -checked=>'on'), $cgi->p,
335 : redwards 1.1 $cgi->checkbox(-name=>"levels", -label=>"Show subsystem classification", -checked=>'on'), $cgi->p,
336 :     $cgi->checkbox(-name=>"genomes", -label=>"Show genomes in subsystem", -checked=>'on'), $cgi->p,
337 : redwards 1.4 $cgi->checkbox(-name=>"haveroles", -label=>"Show only subsystems that have roles defined"), $cgi->p,
338 :     $cgi->checkbox(-name=>"orgpegs", -label=>"Show only subsystems that have roles in the organism(s) you have chosen"), $cgi->p,
339 : redwards 1.3
340 : redwards 1.1 $cgi->end_form,
341 :    
342 :     }

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