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MoleculePage.pl
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MoleculePage.pl
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#!/usr/local/bin/perl
# Copyright SRA International
#
# Distributed under the OSI-approved BSD 3-Clause License.
# See http://ncip.github.com/pathway-interaction-database/LICENSE.txt for details.
######################################################################
# MoleculePage.pl
#
# internal molecule id
# external molecule ids
# molecule names
# used-in-complex table:
# used-in-atom table:
# check to include
# role (input, output, agent, inhibitor)
# location
# state
# atom (hyperlink)
# pathway (hyperlink)
# source
#
BEGIN {
my @path_elems = split("/", $0);
pop @path_elems;
push @INC, join("/", @path_elems);
}
use strict;
use CGI;
use Pathway;
use PWLabel;
use PathwayDB;
use DBI;
if (-d "/app/oracle/product/dbhome/current") {
$ENV{'ORACLE_HOME'} = "/app/oracle/product/dbhome/current";
} elsif (-d "/app/oracle/product/8.1.7") {
$ENV{'ORACLE_HOME'} = "/app/oracle/product/8.1.7";
} elsif (-d "/app/oracle/product/8.1.6") {
$ENV{'ORACLE_HOME'} = "/app/oracle/product/8.1.6";
}
my $query = new CGI;
my $base = $query->param("BASE");
my $molid = $query->param("molid");
my $BASE;
##!!!!! for now:
my $LIMIT_SOURCES = "1,2,3,5";
my (%atom_uses, %complex_uses, %location, %state,
%atom2pathway, %atom2source, %pathway2name, %pathway2source);
my ($db_inst, $db_user, $db_pass, $schema) =
("cgprod", "web", "readonly", "cgap");
my $db = DBI->connect("DBI:Oracle:" . $db_inst, $db_user, $db_pass);
if (not $db or $db->err()) {
print STDERR "Cannot connect to " . $db_user . "@" . $db_inst . "\n";
exit;
}
my $lv = new PWLabel($db, $schema);
my $pw = new Pathway($lv);
my $pdb = new PathwayDB($db, $schema, $LIMIT_SOURCES, $pw, $lv);
my $COMPLEX_TYPE = $lv->StringToLabelValue("molecule-type", "complex");
my $PROTEIN_TYPE = $lv->StringToLabelValue("molecule-type", "protein");
my $RNA_TYPE = $lv->StringToLabelValue("molecule-type", "rna");
my $COMPOUND_TYPE = $lv->StringToLabelValue("molecule-type", "compound");
print "Content-type: text/html\n\n";
print "<html>\n";
print "<head><title>Molecule Page</title></head>\n";
print "<body>\n";
MoleculePage_1 ($base, $db, $schema, $molid);
$db->disconnect();
######################################################################
sub LL_URL {
my ($locus) = @_;
return "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?" .
"db=gene&cmd=Retrieve&dopt=Graphics&" .
"list_uids=$locus";
}
######################################################################
sub MOLPAGE_URL {
my ($molid) = @_;
return "$BASE/cgi-bin/MoleculePage?" .
"molid=$molid";
}
######################################################################
sub ATOM_URL {
my ($atomid) = @_;
return "$BASE/DrawPathway?" .
"atom_id=$atomid&what=graphic&svg=on";
}
######################################################################
sub PATHWAY_URL {
my ($pathwayid) = @_;
return "$BASE/DrawPathway?" .
"pathway_id=$pathwayid&what=graphic&svg=on";
}
######################################################################
sub MoleculePage_1 {
my ($base, $db, $schema, $molid) = @_;
$BASE = $base;
$pdb->AtomsOfMols($molid);
SimpleOrComplex($molid);
PathwayAndSource($db, $schema);
IdStuff($molid);
GOStuff($molid);
ComplexTable($molid);
AtomTable($molid);
}
######################################################################
sub GOStuff {
my ($molid) = @_;
my ($db_inst, $db_user, $db_pass, $schema) =
("lpgdev", "web", "readonly", "schaefec");
my ($locus);
my ($sql, $stm);
my ($go_id, $go_name, $evidence, @lines);
my $db = DBI->connect("DBI:Oracle:" . $db_inst, $db_user, $db_pass);
if (not $db or $db->err()) {
print STDERR "Cannot connect to " . $db_user . "@" . $db_inst . "\n";
exit;
}
my $ehash = $pw->MolExId($molid);
for my $id_type (keys %{ $ehash }) {
for my $id (keys %{ $$ehash{$id_type} }) {
if ($id_type eq "LL") {
$locus = $id;
}
}
}
if (! defined $locus || ! $locus) {
return;
}
$sql = qq!
select unique
n.go_id,
n.go_name,
s.evidence
from
$schema.go_name n,
$schema.sptr_goa s,
$schema.ll2sp l
where
l.ll_id = $locus
and l.sp_primary = s.sp_id
and s.go_id = n.go_id
and n.go_class = 'MF'
order by
s.evidence, n.go_name
!;
$stm = $db->prepare($sql);
if(not $stm) {
print STDERR "$sql\n";
print STDERR "$DBI::errstr\n";
print STDERR "prepare call failed\n";
exit;
}
if(!$stm->execute()) {
print STDERR "$sql\n";
print STDERR "$DBI::errstr\n";
print STDERR "execute call failed\n";
exit;
}
while (($go_id, $go_name, $evidence) = $stm->fetchrow_array()) {
push @lines, "<tr><td>GO:$go_id</td><td>$go_name</td><td>$evidence</td></tr>";
}
if (@lines) {
print "<p>GO Molecular Function Annotations:\n";
print "<blockquote>\n";
print "<p><table border=1 cellspacing=1 cellpadding=4>\n";
print "<tr><td><b>GO Id</b></td><td><b>GO Name</b></td><td><b>Evidence</b></td></tr>\n";
print join("\n", @lines) . "\n";
print "</table>\n";
print "</blockquote>\n";
}
$db->disconnect();
}
######################################################################
sub PathwayAndSource {
my ($db, $schema) = @_;
my ($sql, $stm);
my (%pathways);
my ($atom_id, $pathway_id, $pathway_name, $source);
$sql = "select pa.atom_id, pa.pathway_id " .
"from $schema.pw_pathway_atom pa, $schema.pw_atom a " .
"where pa.atom_id in (" . join(",", keys %atom_uses) . ") " .
"and a.atom_source_id in ($LIMIT_SOURCES)";
$stm = $db->prepare($sql);
if(not $stm) {
print STDERR "$sql\n";
print STDERR "$DBI::errstr\n";
print STDERR "prepare call failed\n";
exit;
}
if(!$stm->execute()) {
print STDERR "$sql\n";
print STDERR "$DBI::errstr\n";
print STDERR "execute call failed\n";
exit;
}
while (($atom_id, $pathway_id) = $stm->fetchrow_array()) {
$atom2pathway{$atom_id}{$pathway_id} = 1;
$pathways{$pathway_id} = 1;
}
$sql = "select a.atom_id, s.source_name from $schema.pw_atom a, " .
"$schema.pw_source s " .
"where a.atom_id in (" . join(",", keys %atom_uses) . ") " .
"and a.atom_source_id = s.source_id";
$stm = $db->prepare($sql);
if(not $stm) {
print STDERR "$sql\n";
print STDERR "$DBI::errstr\n";
print STDERR "prepare call failed\n";
exit;
}
if(!$stm->execute()) {
print STDERR "$sql\n";
print STDERR "$DBI::errstr\n";
print STDERR "execute call failed\n";
exit;
}
while (($atom_id, $source) = $stm->fetchrow_array()) {
$atom2source{$atom_id} = $source;
}
$sql = "select p.pathway_id, p.pathway_name, s.source_name " .
"from $schema.pw_pathway p, $schema.pw_source s " .
"where p.pathway_id in (" . join(",", keys %pathways) . ") " .
"and p.pathway_source_id = s.source_id";
$stm = $db->prepare($sql);
if(not $stm) {
print STDERR "$sql\n";
print STDERR "$DBI::errstr\n";
print STDERR "prepare call failed\n";
exit;
}
if(!$stm->execute()) {
print STDERR "$sql\n";
print STDERR "$DBI::errstr\n";
print STDERR "execute call failed\n";
exit;
}
while (($pathway_id, $pathway_name, $source) = $stm->fetchrow_array()) {
$pathway2source{$pathway_id} = $source;
$pathway2name{$pathway_id} = $pathway_name;
}
}
######################################################################
sub IdStuff {
my ($molid) = @_;
my (@names, @ids, $locus);
my $nhash = $pw->MolName($molid);
for my $name_type (keys %{ $nhash }) {
for my $name (keys %{ $$nhash{$name_type} }) {
push @names, $name;
}
}
my ($label, $moltype) = $lv->LabelValueToString($pw->MolType($molid));
if ($moltype eq "complex") {
unshift @names, "<cx_$molid>";
}
my $ehash = $pw->MolExId($molid);
for my $id_type (keys %{ $ehash }) {
for my $id (keys %{ $$ehash{$id_type} }) {
if ($id_type eq "LL") {
$locus = $id;
} else {
push @ids, $id;
}
}
}
print "<p>Basic identification:\n";
print "<blockquote>\n";
print "<p><table border=1 cellspacing=1 cellpadding=4>\n";
print "<tr><td>Molecule Id:</td><td>$molid</td></tr>\n";
print "<tr><td>Molecule type:</td><td>$moltype</td></tr>\n";
print "<tr><td>Names:</td><td>" . join(", ", sort @names) . "</td></tr>\n";
if ($locus) {
print "<tr><td>Entrez Gene:</td><td><a href=\"" . LL_URL($locus) . "\"" .
">$locus</a></td></tr>\n";
}
if (@ids) {
print "<tr><td>Other ids:</td><td>" . join(", ", sort @ids) . "</td></tr>\n";
}
print "</table>\n";
print "</blockquote>\n";
}
######################################################################
sub ComplexTable {
my ($molid) = @_;
my ($label, $value);
my ($cx, $m, @temp);
if (scalar(keys %complex_uses) == 0) {
return;
}
print "<p>Uses in complexes:\n";
print "<blockquote>\n";
print "<p><table border=1 cellspacing=1 cellpadding=4>\n";
print "<tr><td>Complex</td><td>Other Components</td></tr>\n";
for $cx (keys %complex_uses) {
undef @temp;
print "<tr><td><a href=\"" .
MOLPAGE_URL($cx) . "\"><cx_$cx></a></td><td>";
for my $m (keys %{ $complex_uses{$cx} }) {
if ($m != $molid) {
push @temp, ("<a href=\"" . MOLPAGE_URL($m) . "\">" .
$pw->PickMolName($m) . "</a>");
}
}
print join(", ", @temp);
print "</td></tr>\n";
}
print "</table>\n";
print "</blockquote>\n";
}
######################################################################
sub AtomTable {
my ($molid) = @_;
my ($label, $value);
my ($atom, $edge);
my (@pids, $pathwayid, $pcell, $atomtype);
my ($location, $state, $role, $source);
my %tmp;
print "<p>Interactions:\n";
print "<blockquote>\n";
print "<p><table border=1 cellspacing=1 cellpadding=4>\n";
print "<tr>" .
"<td><b>Role</b></td>" .
"<td><b>Location</b></td>" .
"<td><b>State</b></td>" .
"<td><b>Interaction</b></td>" .
"<td><b>Pathway</b></td>" .
"<td><b>Source</b></td>" .
"</tr>\n";
for $atom (keys %atom_uses) {
($label, $atomtype) =
$lv->LabelValueToString($pw->AtomType($atom));
@pids = keys %{ $atom2pathway{$atom} };
if (@pids == 0) {
$pids[0] = "";
}
for $edge (keys %{ $atom_uses{$atom} }) {
for $pathwayid (@pids) {
if ($pathwayid) {
$pcell =
"<a href=\"" . PATHWAY_URL($pathwayid) .
"\">$pathway2name{$pathwayid}</a>";
$source = $pathway2source{$pathwayid};
} else {
$pcell = " ";
$source = $atom2source{$atom};
}
$role = $atom_uses{$atom}{$edge};
$location = $location{$atom}{$edge};
$location or $location = " ";
$state = $state{$atom}{$edge};
$state or $state = " ";
$source or $source = " ";
push @{ $tmp{"$role|$location|$state|"} }, "<tr><td>" .
join("</td>\n<td>",
$role,
$location,
$state,
"$atomtype (<a href=\"" . ATOM_URL($atom) . "\">$atom</a>)",
$pcell,
$source
) . "</td></tr>\n";
}
}
}
for my $i (sort keys %tmp) {
for (@{ $tmp{$i} }) {
print $_;
}
}
print "</table>\n";
print "<p><a href=\"" . ATOM_URL(join(",", keys %atom_uses)) .
"\">Display all interactions</a>";
print "</blockquote>\n";
}
######################################################################
sub SimpleOrComplex {
my ($molid) = @_;
my ($atom, $edge, $m, $lvid, $label, $value, $edgetype);
for $atom (@{ $pw->Atoms() }) {
for $edge (@{ $pw->Edges($atom) }) {
$m = $pw->EdgeMol($atom, $edge);
if ($m == $molid) {
$edgetype = $pw->EdgeType($atom, $edge);
($label, $value) = $lv->LabelValueToString($edgetype);
$atom_uses{$atom}{$edge} = $value;
for $lvid (@{ $pw->MolLabel($atom, $edge) }) {
($label, $value) = $lv->LabelValueToString($lvid);
if ($label eq "location") {
$location{$atom}{$edge} = $value;
} elsif ($label eq "activity-state") {
$state{$atom}{$edge} = $value;
}
}
}
if ($pw->MolType($m) == $COMPLEX_TYPE) {
my %accum;
LeafComponents($m, \%accum);
if (defined $accum{$molid}) {
for my $c (keys %accum) {
$complex_uses{$m}{$c} = 1;
}
}
}
}
}
}
######################################################################
sub LeafComponents {
my ($molid, $accum) = @_;
my ($seq, $m);
if ($pw->MolType($molid) != $COMPLEX_TYPE) {
return;
}
for $seq (@{ $pw->Components($molid) }) {
$m = $pw->ComponentMol($molid, $seq);
if (! defined $$accum{$m}) {
$$accum{$m} = 1;
if ($pw->MolType($m) == $COMPLEX_TYPE) {
LeafComponents($m, $accum);
}
}
}
}