[Bio] / FigWebServices / subsys_summary.cgi Repository:
ViewVC logotype

Annotation of /FigWebServices/subsys_summary.cgi

Parent Directory Parent Directory | Revision Log Revision Log


Revision 1.5 - (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 $tablerows;
111 : redwards 1.2
112 : redwards 1.1 # get the classification if required
113 :     if ($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, $rows];
135 : redwards 1.3 }
136 : redwards 1.2
137 : redwards 1.3
138 :     #
139 :     # This is convolvuted because we may want to skip some empty cells, but we won't know whether
140 :     # we want to skip them. Also, we are using rowspan/colspan to determine the size of the cells
141 :     # so we need everything defined
142 :     #
143 :     # I store the table initially in @$tablerows, and then push it into @$table. Later on we
144 :     # reconstruct @$table with <td> etc....
145 :     #
146 :     # Now I am going to store the rows in @$toadd, and if we want them I will add them to @$table.
147 :     #
148 :     # For stats, there is only one row in @$toadd, but for other data there are several because
149 :     # of the use of rowspan
150 :    
151 :     my $pegcount;
152 :     my $toadd; #this is what we will add if we need to
153 : redwards 1.2 if ($cgi->param('stats')) {
154 : redwards 1.4 push @$tablerows, [(scalar @roles), '1', $rows];
155 : redwards 1.3 my $totalpegs;
156 : redwards 1.2 # there should be a quicker way of getting this ... ?
157 :     foreach my $role (@roles) {
158 :     foreach my $genome (keys %genomes) {
159 :     my $count = scalar ($fig->pegs_in_subsystem_cell($subsys, $genome, $role));
160 :     $pegcount->{$genome} += $count;
161 :     $totalpegs += $count;
162 :     }
163 :     }
164 : redwards 1.3
165 : redwards 1.4 push @$tablerows, [$totalpegs, '1', $rows];
166 : redwards 1.2 foreach my $w (@wants) {
167 : redwards 1.4 push @$tablerows, [$pegcount->{$w}, '1', $rows]; # pegs for each of the chosen genomes
168 : redwards 1.2 }
169 : redwards 1.3 push @$toadd, $tablerows;
170 : redwards 1.2 }
171 : redwards 1.3 elsif ($cgi->param('korgs')) {
172 : redwards 1.1 my $first=1;
173 :     foreach my $role (@roles) {
174 : redwards 1.5 if ($role eq "Membrane Transport") {print STDERR "Found role Membrane Transport in $subsys\n"}
175 : redwards 1.1 my $genomeroles;
176 :     foreach my $gen (@wants) {
177 : redwards 1.2 my $cell = ' &nbsp; ';
178 : redwards 1.1 if ($genomes{$gen}) {
179 :     foreach my $peg ($fig->pegs_in_subsystem_cell($subsys, $gen, $role)) {
180 :     $cell .= &HTML::fid_link($cgi,$peg) . "; ";
181 :     }
182 :     }
183 : redwards 1.4 push @$genomeroles, [$cell, 1, 1];
184 : redwards 1.1 }
185 :     # because I am using rowspan to make long columns, we don't want the tr on the first of these.
186 : redwards 1.3 if ($first) {
187 : redwards 1.4 push @$tablerows, ([$role, 1, 1], @$genomeroles);
188 :     push @$toadd, @$tablerows;
189 :     undef $first;
190 : redwards 1.3 }
191 :     else {
192 : redwards 1.4 my @tr=([$role, 1, 1], @$genomeroles);
193 :     push @$toadd, \@tr;
194 : redwards 1.3 }
195 : redwards 1.1 }
196 :     }
197 : redwards 1.5
198 :     unless ($toadd) {
199 :     push @$toadd, @$tablerows;
200 :     print STDERR "For $subsys just defined ", join " ", @$toadd, "\n";
201 :     } # in case we didn't define it
202 :    
203 :    
204 : redwards 1.3 # now decide if we want the table
205 :     if ($cgi->param('orgpegs')) {
206 :     my $mustadd;
207 :     foreach my $org (@wants) {if ($pegcount->{$org}) {$mustadd=1}} # we'll add it if one of the orgs has a role
208 :     if ($mustadd) {push @$table, @$toadd}
209 :     }
210 :     elsif ($cgi->param("haveroles")) {
211 :     if (scalar(@roles)) {push @$table, @$toadd}
212 :     }
213 :     else {
214 :     push @$table, @$toadd;
215 :     }
216 :     }
217 :    
218 :     # now convert $table into a table
219 : redwards 1.4
220 :     # sort the table
221 :     # if we have levels we want to sort on level 1 and then level 2 and then subsysname
222 :     # if not, we just sort on subsys name
223 :     if ($cgi->param("levels")) {
224 :     @$table = sort {
225 :     $a->[0]->[0] cmp $b->[0]->[0]
226 :     ||
227 :     $a->[1]->[0] cmp $b->[1]->[0]
228 :     ||
229 :     $a->[2]->[0] cmp $b->[2]->[0]
230 :     } @$table;
231 :     }
232 :     else {
233 :     @$table = sort {
234 :     $a->[0]->[0] cmp $b->[0]->[0]
235 :     } @$table;
236 :     }
237 :    
238 :    
239 : redwards 1.3 my $tab;
240 :     foreach my $row (@$table) {
241 :     $tab .= "\n<tr>";
242 :     foreach my $cell (@$row) {
243 : redwards 1.4 unless (ref($cell) eq "ARRAY") {
244 :     print STDERR "Didn't work. This is what we have for the row: ", join "\n", @$row, "\n";
245 :     exit(-1);
246 :     }
247 : redwards 1.5 my $width='';
248 :     if ($cell->[3]) {$width="width " . $cell->[3]}
249 :     $tab .= "\n\t<td valign=top $width colspan=$cell->[1] rowspan=$cell->[2]>$cell->[0]</td>";
250 : redwards 1.3 }
251 :     $tab .= "\n</tr>\n";
252 : redwards 1.1 }
253 : redwards 1.3
254 :     push @$html, ("\n<table border=1>" . $tableheader . $tab . "</table>\n");
255 : redwards 1.1 }
256 :    
257 :    
258 :    
259 :    
260 :    
261 :    
262 :    
263 :    
264 :    
265 :    
266 :     sub show_initial {
267 :     #############
268 :     #
269 :     # Stolen from index.cgi
270 :     #
271 :     #
272 :    
273 :     my @display = ( 'All', 'Archaea', 'Bacteria', 'Eucarya', 'Viruses', 'Environmental samples' );
274 :    
275 :     #
276 :     # Canonical names must match the keywords used in the DBMS. They are
277 :     # defined in compute_genome_counts.pl
278 :     #
279 :     my %canonical = (
280 :     'All' => undef,
281 :     'Archaea' => 'Archaea',
282 :     'Bacteria' => 'Bacteria',
283 :     'Eucarya' => 'Eukaryota',
284 :     'Viruses' => 'Virus',
285 :     'Environmental samples' => 'Environmental Sample'
286 :     );
287 :    
288 :     my $req_dom = $cgi->param( 'domain' ) || 'All';
289 :     my @domains = $cgi->radio_group( -name => 'domain',
290 :     -default => $req_dom,
291 :     -override => 1,
292 :     -values => [ @display ]
293 :     );
294 :    
295 :     my $n_domain = 0;
296 :     my %dom_num = map { ( $_, $n_domain++ ) } @display;
297 :     my $req_dom_num = $dom_num{ $req_dom } || 0;
298 :    
299 :     #
300 :     # Viruses and Environmental samples must have completeness = All (that is
301 :     # how they are in the database). Otherwise, default is Only "complete".
302 :     #
303 :     my $req_comp = ( $req_dom_num > $dom_num{ 'Eucarya' } ) ? 'All'
304 :     : $cgi->param( 'complete' ) || 'Only "complete"';
305 :     my @complete = $cgi->radio_group( -name => 'complete',
306 :     -default => $req_comp,
307 :     -override => 1,
308 :     -values => [ 'All', 'Only "complete"' ]
309 :     );
310 :     #
311 :     # Use $fig->genomes( complete, restricted, domain ) to get org list:
312 :     #
313 :     my $complete = ( $req_comp =~ /^all$/i ) ? undef : "complete";
314 :    
315 :     my @orgs = sort map { my $org = $_; my $gs = $fig->genus_species($org); my $gc=scalar $fig->all_contigs($org); "$gs ($org) [$gc contigs]" }
316 :     $fig->genomes( $complete, undef, $canonical{ $req_dom } );
317 :    
318 :     my $n_genomes = @orgs;
319 :    
320 :     push @$html, $cgi->start_form,
321 :     $cgi->h2("Please choose one or more organisms from the list below to see in the subsystems table"),
322 :     "<TABLE>\n",
323 :     " <TR>\n",
324 :     " <TD>",
325 :     $cgi->scrolling_list( -name => 'korgs',
326 :     -size => 10,
327 :     -multiple => 1,
328 :     -values => \@orgs,
329 :     ),
330 :     $cgi->br,
331 :     "$n_genomes genomes shown ",
332 :     $cgi->submit( 'Update List' ), $cgi->reset, $cgi->submit('submit', 'Summarize Subsystems'),
333 :     "</TD>",
334 :     " <TD>",
335 :     join( "<br>", "<b>Domain(s) to show:</b>", @domains), "<br>\n",
336 :     join( "<br>", "<b>Completeness?</b>", @complete), "\n",
337 :     "</TD>",
338 :     " </TR>\n",
339 :     "</TABLE>\n",
340 :     $cgi->p,
341 : redwards 1.2 $cgi->checkbox(-name=>"stats", -label=>"Only show statistics", -checked=>'on'), $cgi->p,
342 : redwards 1.1 $cgi->checkbox(-name=>"levels", -label=>"Show subsystem classification", -checked=>'on'), $cgi->p,
343 :     $cgi->checkbox(-name=>"genomes", -label=>"Show genomes in subsystem", -checked=>'on'), $cgi->p,
344 : redwards 1.4 $cgi->checkbox(-name=>"haveroles", -label=>"Show only subsystems that have roles defined"), $cgi->p,
345 :     $cgi->checkbox(-name=>"orgpegs", -label=>"Show only subsystems that have roles in the organism(s) you have chosen"), $cgi->p,
346 : redwards 1.3
347 : redwards 1.1 $cgi->end_form,
348 :    
349 :     }

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3