-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathspecies_db_queries3.php
286 lines (274 loc) · 14.4 KB
/
species_db_queries3.php
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
<?php
// this script collects species-specific information for display as checkboxes
// this is version 2 of the script
// original for nembase4 September 2007
// also used in NEMBASE4 September 2008
// original written by Ann Hedley, University of Edinburgh
// version 2 by Ben Elsworth and Mark Blaxter, University of Edinburgh
##################
#ben 21/07/08
#couldn't connect to search_results.shtml/php to view clusters from species_info.php
#search_results.shtml/php was not in nembase4, copied over from nemdb3/probably_junk!!!
#see line 97
#20/08/08
#removed 'view all clusters' button and replaced with text link
#################
//open the database
$PG_HOST="localhost";
$PG_PORT=5432;
$PG_DATABASE2="species_db4";
$PG_USER="webuser";
$PG_PASS="";
$dbconn=pg_connect( "dbname=$PG_DATABASE2 host=$PG_HOST port=$PG_PORT user=$PG_USER password=$PG_PASS" );
if ( ! $dbconn ) {
echo "Error connecting to the database !<br> " ;
printf("%s", pg_errormessage( $dbconn ) );
exit();
}
#$ref=$_SERVER['DOCUMENT_NAME'];print "* $ref<br><br>\n";############
if ($_SERVER['DOCUMENT_NAME'] && preg_match("/index/",$_SERVER['DOCUMENT_NAME'])) {overall_stats($dbconn,"index");}
elseif ($_SERVER['DOCUMENT_NAME'] && preg_match("/overview/",$_SERVER['DOCUMENT_NAME'])) {overall_stats($dbconn,"overview");overview($dbconn);}
elseif ($_SERVER['PHP_SELF'] && preg_match("/libSpec.php/",$_SERVER['PHP_SELF'])) {dropdown_list($dbconn);}
elseif ($_SERVER['PHP_SELF'] && preg_match("/species_info.php/",$_SERVER['PHP_SELF'])) {details_for_sp($dbconn);}
else {clades($dbconn);}
###########################################################################################################
############### Sub routines ###############
###########################################################################################################
# This routine calls the species list as a dropdown choice list
function dropdown_list($dbconn) {
$sqlcom="select distinct spec_id,name from info;";
$dbres = pg_exec($dbconn, $sqlcom );
if ( ! $dbres ) {echo "Error : " + pg_errormessage( $dbconn ); exit();}
$row=0;
$rowmax=pg_NumRows($dbres);
print "<form method=\"post\" action=\"libSpec.php\"><select name=\"organism\" onchange=\"this.form.submit();\">\n<option value=\"select\">Select an organism...</option>\n";
while ($row<$rowmax) {
$do = pg_Fetch_Object($dbres, $row);
$name=$do->name;
print "<option value=\"$name\">$name</option>\n";
$row++;
}
print("</select></form>\n\n");
}
function details_for_sp($dbconn) {
// Get species id
$sp=$_REQUEST["species"];
$sqlcom="select name,short_des,long_des,lifecyc,taxonomy,links,clade,num_seq,num_clus,num_lib from info natural join stats where spec_id='$sp';";
$dbres = pg_exec($dbconn, $sqlcom );
if ( ! $dbres ) {echo "Error : " + pg_errormessage( $dbconn ); exit();}
$do = pg_Fetch_Object($dbres, 0);
$name=$do->name;
$short=$do->short_des;
$long=$do->long_des;
$lifecyc=$do->lifecyc;
$taxonomy=$do->taxonomy;
$links=$do->links;
$clade=$do->clade;
$num_seq=$do->num_seq;
$num_clus=$do->num_clus;
$num_lib=$do->num_lib;
if (file_exists("/var/www/html/nembase4/species/$sp.jpg")) {$image=$sp.".jpg";}else{$image=$sp.".gif";}
print "<table cellspacing=0 cellpadding=3 border=0><tr>\n";
print "<td><IMG SRC=\"/nembase4/species/$image\" WIDTH=150 HEIGHT=150 ALIGN=bottom></td>\n";
print "<td width=300><I>$name</I>";
if ($short!="") {print "<br>($short)<br><br>\n";}else{print "<br><br><br>\n";}
print "<A HREF=\"/nembase4/search_results.shtml?organism=$sp\" target=\"_top\" ";
print " onMouseOver=\"hiLite('img01','but2')\" onMouseOut=\"hiLite('img01','but1')\">\n";
print "<IMG ALT=\"View all clusters\" NAME=\"img01\" SRC=\"/nembase4/species/viewall_nembase4.jpg\" width=150 height=40 border=0></A>\n";
print "</td></tr></table><hr>\n";
if ($long!="") {print "<table cellspacing=0 cellpadding=3 border=0><tr><td>Description</td></tr><tr><td><I>$name</I> $long</td></tr></table><hr>\n";}
if ($lifecyc!="") {print "<table cellspacing=0 cellpadding=3 border=0><tr><td>Lifecycle</td></tr><tr><td>$lifecyc</td></tr></table><hr>\n";}
print "<table cellspacing=0 cellpadding=3 border=0><tr><td width=450 colspan=2>Details</td></tr>"\n;
print "<tr><td>Total number of sequences</td><td>$num_seq</td></tr>\n";
print "<tr><td>Number of NEMBASE clusters</td><td>$num_clus</td>\n";
print "</tr><tr><td>Number of Libraries</td><td>$num_lib</td></tr>\n";
print "<tr><td>Phylogeny</td><td><a href=\"/nembase4/clade$clade.shtml\" target=\"_top\">Clade $clade</a></td></tr>\n";
print "<tr valign=top><td>Links</td><td><a href=\"/nembase4/index.shtml\" target=\"_top\">NEMBASE</A><br>\n";
print "<a href=\"/nembase4/stats.shtml\" target=\"_top\">Library statistics</A><br>$links</td>\n";
print "</tr></table>\n";
$sqlcom="select seq_cent,e_name,email from org where spec_id='$sp';";
$dbres = pg_exec($dbconn, $sqlcom );
if ( ! $dbres ) {echo "Error : " + pg_errormessage( $dbconn ); exit();}
$row=0;
$rowmax=pg_NumRows($dbres);
if ($rowmax>0) {print "<hr><table><tr valign=top><td colspan=2>Contacts</td><td></td></tr>\n";}
while ($row<$rowmax) {
$do = pg_Fetch_Object($dbres, $row);
$seq_cent=$do->seq_cent;
$e_name=$do->e_name;
$email=$do->email;
if ($email!="") {$mail_link="<a href=\"mailto:$email\">$e_name</a>";}
else {$mail_link="$e_name";}
print "<tr><td>$seq_cent</td><td>$mail_link</td></tr>\n";
$row++;
}
print "</table>\n";
}
###########################################################################################################
# this subroutine queries species_db4 for overall statistics for the whole database
function overall_stats($dbconn,$page) {
$sqlcom="select count(distinct spec_id),sum(num_seq) as seqs,sum(num_clus) as clus,sum(num_lib) as libs,max(last_update),max(anno_update) as anno from stats;";
$dbres = pg_exec($dbconn, $sqlcom );
if ( ! $dbres ) {echo "Error : " + pg_errormessage( $dbconn );exit();}
$do = pg_Fetch_Object($dbres, $row);
$count=$do->count;
$seqs=$do->seqs;$seqs=number_format($seqs);
$clus=$do->clus;$clus=number_format($clus);
$libs=$do->libs;$libs=number_format($libs);
$update=$do->max;preg_match("/^(\d\d\d\d)-(\d\d)-\d\d/","$update", $date);
$anno_update=$do->anno;preg_match("/^(\d\d\d\d)-(\d\d)-\d\d/","$anno_update", $anno_date);
if ($page=="index") {
print "<tr><td>Last annotation update</td><td>$anno_date[2] / $anno_date[1]</td></tr>\n";
print "<tr><td>Last sequence update</td><td>$date[2] / $date[1]</td></tr>\n";
print "<tr><td>Number of Species</td><td align=\"right\">$count</td></tr>\n";
print "<tr><td>Number of Libraries   </td><td align=\"right\">$libs</td></tr>\n";
print "<tr><td>Number of Clusters</td><td align=\"right\">$clus</td></tr>\n";
print "<tr><td>Number of ESTs</td><td align=\"right\">$seqs</td></tr>\n";
}
else {
print "<tr><td class=\"mainBig\" colspan=8><br>Last data update $date[2] / $date[1]";
print ": NEMBASE4 contains data for $count Species, from $libs libraries, $clus clusters and $seqs ESTs<br><br></td></tr><tr>\n";
}
}
###########################################################################################################
# this subroutine retrieves precalculated stats for each species
function overview($dbconn) {
$sqlcom="select info.spec_id,name,num_seq,num_clus,num_lib,last_update from info natural join stats;";
$dbres = pg_exec($dbconn, $sqlcom );
if ( ! $dbres ) {
echo "Error : " + pg_errormessage( $dbconn );
exit();
}
$row=0;
$rowmax=pg_NumRows($dbres);
while ($row<$rowmax) {
$do = pg_Fetch_Object($dbres, $row);
$spec_id=$do->spec_id;
$species=$do->name;$species = preg_replace('/ /','<br>',$species,1);
$seqs=$do->num_seq;$seqs=number_format($seqs);
$clus=$do->num_clus;$clus=number_format($clus);
$libs=$do->num_lib;$libs=number_format($libs);
$update=$do->last_update;preg_match("/^(\d\d\d\d)-(\d\d)-\d\d/","$update", $date);
if (file_exists("/var/www/html/nembase4/species/$spec_id.jpg")) {$image=$spec_id.".jpg";}else{$image=$spec_id.".gif";}
print "<td class=\"mainSmall\"><i><a href=\"/nembase4/species_info.php?species=$spec_id\">\n";
print "<img src=\"/nembase4/species/$image\" width=100 height=100>\n";
if ($libs==0) {$plural_libs="libraries documented";}
elseif ($libs>=2) {$plural_libs="libraries";}
else {$plural_libs="library";}
print "</a><br>$species</i><br>updated $date[2]/$date[1]<br>$libs $plural_libs<br>$clus clusters<br>$seqs ESTs<br>\n";
print "<a href=\"/downloads_area/databases/nembase4/$spec_id.fsa\">download clusters</a></td>\n";
$row++;
if ($row%8==0 && $row<$rowmax) {print "</tr><tr>\n";}
}
print("</tr><tr>\n");
}
###########################################################################################################
# code to build the 'tree' of species - used in many php and shtml pages
#this was supposed to be generic so you could update the database and the code would update the website but
#trying to make it look like a tree has made it too specific and you'll probably have to fiddle with it if
#you add clades
function clades($dbconn) {
$sqlcomC="select distinct clade from info order by clade;";
$sqlcomT="select distinct clade,taxonomy from info where taxonomy!='' order by clade,taxonomy;";
$sqlcomS="select distinct spec_id,name,taxonomy,clade from info order by clade,taxonomy;";
# print first part of species selection table
print "<td>\n\n<!-- Table of species with select buttons derived from species_db_queries.php -->\n";
print "<table class=\"tablephpSpSelect\">\n";
print "<tr><td colspan=6 align=left><span class=\"mainBig\"> Species to search</span>\n";
print "<br><span class=\"mainMed\"> Use the checkboxes to select a taxonomic group of species ";
print "(based on the taxonomy of Blaxter and DeLey),<br>\n";
print " or (on the list below) your own selection of species.</span></td></tr>";
print "<tr><td colspan=4 align=center><input type=checkbox onClick=\"if(this.checked)checkAll(); else clearAll()\" checked><br>All Species</td></tr>\n";
print "<tr><td colspan=4 height=2 >\n";
print " <table width=100%>\n";
print " <tr><td width=6%></td><td class=\"All\" > </td><td width=8%></td></tr>\n";
print " </table>\n";
print " </td>\n";
print "</tr>\n";#bar
$dbres = pg_exec($dbconn, $sqlcomC );if ( ! $dbres ) {echo "Error : " + pg_errormessage( $dbconn ); exit();}
print "<tr>";
$row=0;$rowmax=pg_NumRows($dbres);
#for each clade make a check-box
while ($row<$rowmax) {
$do = pg_Fetch_Object($dbres, $row);
$clade=$do->clade;
$col_span=1; if($clade=="III" || $clade=="IV") {$col_span=2;}
$row_span=1; if($clade=="I") {$row_span=3;}
if ($clade=="I") {
print "<td rowspan=$row_span colspan=$col_span align=center>|<br>\n";
print "<input type=checkbox NAME=\"All[]\" value=\"cladeI\" onClick=\"if(this.checked)checkCladeI(); else clearCladeI()\" checked>\n";
print "<br><div class=\"styleI\"> CladeI </div></td>\n";
print "<td colspan=5 align=center>|<br>\n";
print "<input type=checkbox NAME=\"All[]\" value=\"Rhabditina\" onClick=\"if(this.checked)checkRhabditina(); else clearRhabditina()\" checked>\n";
print "<br><div class=\"styleRhabditina\"> Rhabditina </div></td></tr>\n";
print "<tr><td colspan=5 height=1 >\n";
print "<table width=100%>\n";
print "<tr><td width=17%></td><td class=\"Rhabditina\" > </td>\n";
print "<td width=8%></td></tr>\n";
print "</table></td></tr><tr>\n"; #bar
}
else {print "<td rowspan=$row_span colspan=$col_span align=center>|<br>\n";
print "<input type=checkbox NAME=\"Rhabditina[]\" value=\"$clade\" onClick=\"if(this.checked)check$clade(); else clear$clade()\" checked><br>\n";
print "<div class=\"style$clade\">Clade$clade</div></td>\n";}
$row++;
}
print "</tr><tr>\n";
$row=0;
#for each clade draw a bar
while ($row<$rowmax) {
$do = pg_Fetch_Object($dbres, $row);
$clade=$do->clade;
$col_span=1; if($clade=="III" || $clade=="IV") {$col_span=2;}
print "<td colspan=$col_span height=2 >\n";
print "<table width=100%>\n";
print "<tr><td width=10%></td><td class=\"$clade\" > </td><td width=10%></td></tr>\n";
print "</table></td>\n";
$row++;
}
print "</tr>\n";
print "<tr>";
# collect data for each taxon set in $sub_taxo_row
$dbres = pg_exec($dbconn, $sqlcomT );if ( ! $dbres ) {echo "Error : " + pg_errormessage( $dbconn ); exit();}
$row=0;$rowmax=pg_NumRows($dbres);
$sub_taxo_row="<td align=center>";
while ($row<$rowmax) {
$do = pg_Fetch_Object($dbres, $row);
$clade=$do->clade;
$taxonomy=$do->taxonomy;
if (preg_match("/^(\w+)\.(\w+)/","$taxonomy", $match)) {
$sub_taxo_row.="|<br><input type=checkbox NAME=\"$match[1][]\" value=\"$match[2]\" onClick=\"if(this.checked)check$match[2](); else clear$match[2]()\" checked><br><div class=\"style$match[2]\">$match[2]</div>\n";
}
else {
print "<td align=center>|<br><input type=checkbox NAME=\"$clade";
print "[]\" value=\"$taxonomy\" onClick=\"if(this.checked)check$taxonomy(); else clear$taxonomy()\" checked><br>\n";
print "<div class=\"style$taxonomy\"> $taxonomy </div></td>\n";
if ($row>0) {$sub_taxo_row.="</td><td >\n";}
}
$row++;
}
print "<tr>$sub_taxo_row</td></tr>\n";
print "</table></td></tr>\n";
$dbres = pg_exec($dbconn, $sqlcomS);if ( ! $dbres ) {echo "Error : " + pg_errormessage( $dbconn ); exit();}
$row=0;
$rowmax=pg_NumRows($dbres);
print "<tr height=20></tr>\n";
#now print the species list
print "<tr><td colspan=3>\n<table width=\"100%\"><tr>\n";
while ($row<$rowmax) {
$do = pg_Fetch_Object($dbres, $row);
$name=$do->name;
$spec_id[$row]=$do->spec_id;
# $spec_id[$row]=preg_replace('/(\w\w)C/', '\1P',$spec_id[$row]); #make them all prot then change back to clus for the blast search.
$taxo[$row]=$do->taxonomy;
if ($taxo[$row]=="") {$taxo[$row]=$do->clade;}
if (preg_match("/^\w+\.(\w+)/","$taxo[$row]", $match)) {$taxo[$row]=$match[1];}
print "<td><input TYPE=\"checkbox\" NAME=\"$taxo[$row][]\" value=\"$spec_id[$row]\" checked></input></td>\n";
print "<td class=\"mainMed\"><div class=\"style$taxo[$row]\"><i> $name </i></div></td>\n";
$row++;
if ($row%4==0) {print "</tr>\n<tr>";}
}
if ($row%4!=0) {print("</tr>\n");}
print("</table></td></tr>\n");
}
###########################################################################################################
?>