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PWApp.pm
executable file
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PWApp.pm
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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.
BEGIN {
my @path_elems = split("/", $0);
pop @path_elems;
push @INC, join("/", @path_elems);
}
use strict;
use Scan;
use Pathway;
use PathwayXML;
use PathwayDB;
use PathParams;
use PWLabel;
use PathwayGene;
use FileHandle;
use DOT;
use Math::Trig;
use DBI;
use constant MAX_LONG_LEN => 16384;
my $BASE;
my ($COMPLEX_TYPE, $PROTEIN_TYPE, $COMPOUND_TYPE, $RNA_TYPE);
#my $LIMIT_SOURCES = "1,2";
my $LIMIT_SOURCES = "";
my $LIMIT_EVIDENCE = "";
my @CCF = ( ## common co-factors
'water',
'atp',
'nad',
'nadh',
'nadph',
'nadp',
'oxygen',
'adp',
'orthophosphate',
'coa',
'carbon dioxide',
'diphosphate',
'ammonia',
'h+'
);
my ($db_inst, $db_user, $db_pass, $schema) =
(DB_INST, DB_USER, DB_PASS, SCHEMA);
use constant MAX_DOT_INTERACTIONS => 800;
my $lv;
my %mol2atom;
my %atom2atom;
my %cx2cp;
## dot2xaml constants
my $tangent = tan(deg2rad(60));
my $canvas_n = 0;
my $molCount = 0;
my $keyCount = 1;
my $PIX_PER_INCH = 72;
my $ROUND_CORNER_CLIP = 12;
my $HALF_CORNER_CLIP = 6;
my %TEXT_LINE_INC_Y = (
"10" => 8
);
my %TEXT_LINE_HEAD_ROOM = (
"10" => 13
);
my %TEXT_LINE_FOOT_ROOM = (
"10" => 7
);
my %hex_color = (
"black" => "000000",
"white" => "ffffff",
"red" => "ff0000",
"green" => "00ff00",
"blue" => "0000ff",
"firebrick" => "b22222",
"lightgray" => "736F6E"
);
######################################################################
sub r_numerically { $b <=> $a };
sub numerically { $a <=> $b };
######################################################################
sub SetSchema {
my ($the_schema) = @_;
# as things stand, global $schema acquires value PWAppConfig::SCHEMA
# this sub is to override that value
$schema = $the_schema;
}
######################################################################
sub InitializeLV {
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";
die;
}
$lv = new PWLabel($db, $schema);
$db->disconnect();
$COMPLEX_TYPE = $lv->StringToLabelValue("molecule-type", "complex");
$PROTEIN_TYPE = $lv->StringToLabelValue("molecule-type", "protein");
$RNA_TYPE = $lv->StringToLabelValue("molecule-type", "rna");
$COMPOUND_TYPE = $lv->StringToLabelValue("molecule-type", "compound");
}
######################################################################
sub InitializeComplex2Component {
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 . "@" . $db_inst . "\n";
die;
}
my ($sql, $stm);
my ($cx_id, $cp_id);
$sql = qq!
select
c.complex_mol_id,
c.component_mol_id
from
$schema.pw_complex_component c
!;
$stm = $db->prepare($sql);
if(not $stm) {
print STDERR "$sql\n";
print STDERR "$DBI::errstr\n";
print STDERR "prepare call failed\n";
die;
}
if(!$stm->execute()) {
print STDERR "$sql\n";
print STDERR "$DBI::errstr\n";
print STDERR "execute call failed\n";
die;
}
while (($cx_id, $cp_id) = $stm->fetchrow_array()) {
$cx2cp{$cx_id}{$cp_id} = 1;
}
$stm->finish();
$db->disconnect();
}
######################################################################
sub InitializeAtom2Atom {
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 . "@" . $db_inst . "\n";
die;
}
my ($sql, $stm);
my ($a1, $a2);
$sql = "select * from $schema.pw_connect";
$stm = $db->prepare($sql);
if(not $stm) {
print STDERR "$sql\n";
print STDERR "$DBI::errstr\n";
print STDERR "prepare call failed\n";
die;
}
if(!$stm->execute()) {
print STDERR "$sql\n";
print STDERR "$DBI::errstr\n";
print STDERR "execute call failed\n";
die;
}
while (($a1, $a2) = $stm->fetchrow_array()) {
$atom2atom{$a1}{$a2} = 1;
$atom2atom{$a2}{$a1} = 1;
$atom2atom{$a1}{$a1} = 1;
$atom2atom{$a2}{$a2} = 1;
}
# my %atom2mol;
# my $atom_sources = "";
# my $atom_evidence = "";
# my %ccf;
# CommonCoFactors($db, \%ccf);
# my $prune_mols = join(",", keys %ccf);
# SetUpAtomMatrix($db, $atom_sources, $prune_mols, \%atom2mol, \%mol2atom,
# \%atom2atom, $atom_evidence);
$stm->finish();
$db->disconnect();
}
######################################################################
sub MoleculeName {
my ($pw, $molid) = @_;
my $name = $pw->PickMolName($molid);
# if ($pw->MolType($molid) == $COMPLEX_TYPE) {
# $name = "<" . "cx_$molid" . ">";
# }
return $name;
}
######################################################################
sub Value2Color {
my ($v) = @_;
my @color_scale = (
"0000FF", ## blue = low
"3399FF",
"66CCFF",
"99CCFF",
"CCCCFF", ## skip this -- too close
"",
"FFCCFF", ## skip this -- too close
"FF99FF",
"FF66CC",
"FF6666",
"FF0000" ## red = high
);
my $LO_VAL = 1.0;
my $HI_VAL = 9.0;
my $NORMAL_VAL = ($LO_VAL + $HI_VAL) / 2;
my $delta1 = .25;
my $nlo_colors = 5;
my $nhi_colors = 5;
my $lo_delta = (($NORMAL_VAL - $delta1) - $LO_VAL) / $nlo_colors;
my $hi_delta = ($HI_VAL - ($NORMAL_VAL + $delta1)) / $nhi_colors;
my ($i);
if (($v <= $NORMAL_VAL + $delta1) && ($v >= $NORMAL_VAL - $delta1)) {
return "";
##
## in what follows, use 4 rather than 5 to skip middle colors
##
} elsif ($v < $NORMAL_VAL) {
for ($i = $nlo_colors; $i > 0 ; $i--) {
if ($v < $NORMAL_VAL - $delta1 - (($i-1) * $lo_delta)) {
return "#" . $color_scale[$nlo_colors - $i];
}
}
return "#" . $color_scale[0];
} else {
for ($i = $nhi_colors; $i > 0 ; $i--) {
if ($v > $NORMAL_VAL + $delta1 + (($i-1) * $hi_delta)) {
return "#" . $color_scale[$#color_scale - $nhi_colors + $i];
}
}
return "#" . $color_scale[$#color_scale];
}
}
######################################################################
sub BackTrack {
my ($mazeparent, $endpoint) = @_;
my ($x, @path, %visited);
## NOTE: $endpoint is not part of returned path
## so null path means $endpoint is not in a walk
$x = $endpoint;
while (1) {
## should not be necessary, but ...
if (defined $visited{$x}) {
last;
} else {
$visited{$x} = 1;
}
if (! defined $$mazeparent{$x}) {
last;
} else {
$x = $$mazeparent{$x};
push @path, $x;
}
}
return \@path;
}
######################################################################
sub SetUpAtomMatrix {
my ($db, $atom_sources, $prune_mols, $atom2mol, $mol2atom,
$atom2atom, $atom_evidence) = @_;
my ($sql, $stm);
my ($source_clause, $prune_clause, $evidence_clause);
my ($atom_id, $mol_id);
if ($prune_mols) {
$prune_clause = " and e.mol_id not in ($prune_mols) ";
} else {
$prune_clause = "";
}
if ($atom_sources) {
$source_clause = " and a.atom_source_id in ($atom_sources) ";
} else {
$source_clause = "";
}
if ($atom_evidence) {
$evidence_clause = " and v.evidence_code in ($atom_evidence) ";
} else {
$evidence_clause = "";
}
$sql = qq!
select
e.atom_id,
e.mol_id
from
$schema.pw_edge e,
$schema.pw_atom a,
$schema.pw_evidence v
where
e.atom_id = a.atom_id
and
e.atom_id = v.atom_id
$prune_clause
$source_clause
$evidence_clause
!;
$stm = $db->prepare($sql);
if(not $stm) {
print STDERR "$sql\n";
print STDERR "$DBI::errstr\n";
print STDERR "prepare call failed\n";
die;
}
if(!$stm->execute()) {
print STDERR "$sql\n";
print STDERR "$DBI::errstr\n";
print STDERR "execute call failed\n";
die;
}
while (($atom_id, $mol_id) = $stm->fetchrow_array()) {
$$atom2mol{$atom_id}{$mol_id} = 1;
$$mol2atom{$mol_id}{$atom_id} = 1;
}
$stm->finish();
for my $a1 (keys %{ $atom2mol}) {
for my $m (keys %{ $$atom2mol{$a1} }) {
for my $a2 (keys %{ $$mol2atom{$m} }) {
$$atom2atom{$a1}{$a2} = 1;
$$atom2atom{$a2}{$a1} = 1;
}
}
}
}
######################################################################
sub WalkMaze {
my ($atom2atom, $src, $target, $connection) = @_;
my (%mazeparent);
#print STDERR "WalkMaze: src = " . join(",", keys %{ $src }) . "; " .
# "target = " . join(",", keys %{ $target }) . "\n";
my (%new, %family, $a, $b, $found);
for $a (keys %{ $src }) {
$new{$a} = 1;
}
while (1) {
undef %family;
for $a (keys %new) {
$family{$a} = 1;
}
undef %new;
for $a (keys %family) {
for $b (keys %{ $$atom2atom{$a} }) {
if (defined $$target{$b}) {
$found = $b;
}
if ( !defined $mazeparent{$b} &&
!defined $family{$b} ) { ## no incest
$mazeparent{$b} = $a;
if (! defined $$target{$b}) {
$new{$b} = 1;
}
}
if ($found) {
last;
}
}
if ($found) {
last;
}
}
if ($found || scalar(keys %new) == 0) {
last;
}
}
if ($found) {
$$connection{$found} = 1;
for $a (@{ BackTrack(\%mazeparent, $found) }) {
$$connection{$a} = 1;
}
return 1;
} else {
return 0;
}
}
######################################################################
sub CommonCoFactors {
my ($db, $ccf) = @_;
my ($sql, $stm);
my ($mol_id);
my $namelist = "'" . join("','", @CCF) . "'";
$sql = qq!
select
m.mol_id
from
$schema.pw_mol m,
$schema.pw_mol_name n
where
m.mol_id = n.mol_id
and m.basic_mol_type = 'CM'
and n.mol_name in ($namelist)
!;
$stm = $db->prepare($sql);
if(not $stm) {
print STDERR "$sql\n";
print STDERR "$DBI::errstr\n";
print STDERR "prepare call failed\n";
die;
}
if(!$stm->execute()) {
print STDERR "$sql\n";
print STDERR "$DBI::errstr\n";
print STDERR "execute call failed\n";
die;
}
while (($mol_id) = $stm->fetchrow_array()) {
$$ccf{$mol_id} = 1;
}
$stm->finish();
}
######################################################################
sub FindConnectingPath {
my ($db, $mols_to_join, $source, $molmap) = @_;
my (%src, %target); ## not really directional
my (%connection);
my ($status);
my ($sql, $stm, $atom_id, $mol_id, $mol_type);
####!!!! %mol2atom, %atom2atom are globals
####!!!! %cx2cp is a global
undef %mol2atom;
if (defined $source && keys %{ $source } > 0) {
$sql = "select unique e.atom_id, e.mol_id " .
"from $schema.pw_edge e, " .
"$schema.pw_atom a " .
"where a.atom_id = e.atom_id " .
"and a.atom_source_id in (" .
join(",", keys %{ $source }) .
")";
} else {
$sql = "select unique e.atom_id, e.mol_id " .
"from $schema.pw_edge e ";
}
$stm = $db->prepare($sql);
if(not $stm) {
print STDERR "$sql\n";
print STDERR "$DBI::errstr\n";
print STDERR "prepare call failed\n";
die;
}
if(!$stm->execute()) {
print STDERR "$sql\n";
print STDERR "$DBI::errstr\n";
print STDERR "execute call failed\n";
die;
}
while (($atom_id, $mol_id) = $stm->fetchrow_array()) {
$mol2atom{$mol_id}{$atom_id} = 1;
if (defined $cx2cp{$mol_id}) {
for my $cp_id (keys %{ $cx2cp{$mol_id} }) {
$mol2atom{$cp_id}{$atom_id} = 1;
}
}
}
$stm->finish();
## Take only one mol that matched a query:
## Take the one with the lowest (numerical) id that hits the
## most atoms
my @temp;
for my $q (keys %{ $molmap }) {
my $take_me;
for my $mol (sort numerically keys %{ $$molmap{$q} }) {
if (defined $mol2atom{$mol}) {
if (! defined $take_me) {
$take_me = $mol;
} elsif (scalar(keys %{ $mol2atom{$take_me} }) <
scalar(keys %{ $mol2atom{$mol} })) {
$take_me = $mol;
}
}
}
if (defined $take_me) {
push @temp, $take_me;
}
}
# OLD: take all mols for queried name
# for my $m (sort numerically keys %{ $mols_to_join }) {
# if (defined $mol2atom{$m}) {
# push @temp, $m;
# }
# }
if (@temp < 2) {
for my $a (sort numerically keys %{ $mol2atom{$temp[0]} }) {
$connection{$a} = 1;
last;
}
return \%connection;
}
## do it pairwise
## src is populated with $mol2atom{$temp[$i]} only if there
## is not yet anything in the connection; otherwise, set src = connection
my %hits;
for (my $i = 0; $i < @temp - 1; $i++) {
undef %src;
if (keys %connection == 0) {
for my $atom (keys %{ $mol2atom{$temp[$i]} }) {
$src{$atom} = 1;
}
}
# } else {
# for my $atom (keys %connection) {
# $src{$atom} = 1;
# }
# }
for (my $j = $i + 1; $j < @temp; $j++) {
# if (keys %connection != 0) {
# undef %src;
# for my $a (keys %connection) {
# $src{$a} = 1;
# }
# }
undef %target;
my $already_connected;
for my $a (keys %{ $mol2atom{$temp[$j]} }) {
if (defined $connection{$a}) {
$already_connected++;
last;
}
$target{$a} = 1;
}
if ($already_connected) {
next;
}
for my $a (keys %{ $mol2atom{$temp[$j]} }) {
if (keys %connection == 0 && defined $src{$a}) {
$connection{$a} = 1;
$already_connected++;
last;
}
}
## if any atom for this mol is already in the connection
## move on to the next mol
if ($already_connected) {
next;
}
if (keys %connection == 0) {
$status = WalkMaze(\%atom2atom, \%src, \%target, \%connection);
} else {
$status = WalkMaze(\%atom2atom, \%connection, \%target, \%connection);
}
for my $m (@temp) {
for my $a (keys %{ $mol2atom{$m} }) {
if (defined $connection{$a}) {
$hits{$m} = 1;
last;
}
}
}
if (keys %hits == @temp) {
return \%connection;
}
}
for my $m (@temp) {
for my $a (keys %{ $mol2atom{$m} }) {
if (defined $connection{$a}) {
$hits{$m} = 1;
last;
}
}
}
if (keys %hits == @temp) {
return \%connection;
}
}
## for things that do not connect, just pick one atom
for (my $i = 0; $i < @temp; $i++) {
if (! defined $hits{$temp[$i]}) {
for my $a (sort keys %{ $mol2atom{$temp[$i]} }) {
$connection{$a} = 1;
last;
}
}
}
return \%connection;
}
######################################################################
#
sub TimeStamp {
my ($sec, $min, $hr, $mday, $mon, $year, $wday, $yday, $isdst) =
localtime(time);
my $month = ('Jan', 'Feb', 'Mar', 'Apr', 'May', 'Jun', 'Jul', 'Aug',
'Sep', 'Oct', 'Nov', 'Dec')[$mon];
$year = $year + 1900;
return sprintf "%d_%2.2d_%2.2d_%2.2d_%2.2d_%2.2d",
$year, $mon+1, $mday, $hr, $min, $sec;
}
######################################################################
sub Comment_1 {
my ($base, $name, $email, $organization,
$atomid, $molname, $molid, $pathname, $pathid, $comment) = @_;
my @temp;
push @temp, TimeStamp();
if ( ! open(LOG, ">>" . PW_COMMENT_LOG) ) {
SetStatus(S_RESPONSE_FAIL);
return "Cannot access comment log";
}
for my $x (
$name,
$email,
$organization,
$atomid,
$molname,
$molid,
$pathname,
$pathid,
$comment
) {
$x =~ s/^\s+//;
$x =~ s/\s+$//;
$x =~ s/\t+/ ^TAB^ /;
$x =~ s/\n+/ ^LF^ /;
push @temp, $x;
}
print LOG join("\t", @temp) . "\n";
close LOG;
chmod 0666, PW_COMMENT_LOG;
return "Comment submitted\n";
}
######################################################################
sub SearchMoleculeKeywords_1 {
my ($base, $geneid) = @_;
my (@lines);
$BASE = $base;
my ($db_inst, $db_user, $db_pass, $pid_schema, $cgap_schema) =
(DB_INST, DB_USER, DB_PASS, SCHEMA, "cgap");
$geneid =~ s/\s+//g;
if ($geneid !~ /^\d+$/) {
return "Illegal value for parameter geneid";
}
my $db = DBI->connect("DBI:Oracle:" . $db_inst, $db_user, $db_pass);
if (not $db or $db->err()) {
return "Cannot connect to " . $db_user . "@" . $db_inst . "\n";
}
my ($lv, $pw);
my ($mol2name, $mol2ext_id);
my $mols = FindMolIdsForGene($db, $geneid, $pid_schema, $cgap_schema);
if (keys %{ $mols } > 0) {
($mol2name, $mol2ext_id) = FindNamesForMols($db, $mols, $pid_schema);
} else {
return "No entries for Gene id = $geneid\n";
}
push @lines, FormatOutput($db, $mols, $mol2name, $mol2ext_id, $pid_schema, $geneid);
$db->disconnect;
if (@lines) {
return join("\n", @lines, "");
} else {
return "";
}
}
sub FindMolIdsForGene {
my ($db, $geneid, $pid_schema, $cgap_schema) = @_;
my ($sql, $stm);
my ($molid, $extid);
my (%mols);
## Find direct matches of ext ids
$sql = qq!
select
e.mol_id,
e.ext_mol_id
from
$pid_schema.pw_ext_mol_id e,
$pid_schema.pw_mol m
where
e.ext_mol_id = '$geneid'
and e.mol_id = m.mol_id
and m.basic_mol_type = 'PR'
!;
$stm = $db->prepare($sql);
if(not $stm) {
print STDERR "prepare failed: $sql\n";
return;
}
if(!$stm->execute()) {
print STDERR "execute failed: $sql\n";
return;
}
while (($molid, $extid) = $stm->fetchrow_array()) {
$mols{$molid} = 1;
}
## Find matches of gene ids to proteins in PID
$sql = qq!
select
e.mol_id,
g.ll_id
from
$pid_schema.pw_ext_mol_id e,
$pid_schema.pw_mol m,
$cgap_schema.ll2sp s,
$cgap_schema.sp_primary p,
$cgap_schema.ll_gene g
where
p.sp_id_or_secondary = e.ext_mol_id
and p.sp_id_or_secondary = s.sp_primary
and s.organism = 'Hs'
and s.ll_id = g.ll_id
and g.ll_id ='$geneid'
and e.mol_id = m.mol_id
and m.basic_mol_type = 'PR'
!;
$stm = $db->prepare($sql);
if(not $stm) {
print STDERR "prepare failed: $sql\n";
return;
}
if(!$stm->execute()) {
print STDERR "execute failed: $sql\n";
return;
}
while (($molid, $extid) = $stm->fetchrow_array()) {
$mols{$molid} = 1;
}
return \%mols;
}
sub FormatOutput {
my ($db, $mols, $mol2name, $mol2ext_id, $pid_schema, $gene_id) = @_;
my ($sql, $stm, $source );
my @lines;
push @lines, "Here are molecules corresponding to Entrez Gene ID $gene_id <P>";
for my $mol (keys %{ $mols }) {
my (@lls, @ups, @names);
for my $idtype (keys %{ $$mol2ext_id{$mol} }) {
for my $id (keys %{ $$mol2ext_id{$mol}{$idtype} }) {
if ($idtype eq "LL") {
push @lls, "Entrez Gene: $id";
} elsif ($idtype eq "UP") {
push @ups, "UniProt: $id";
}
}
}
$sql = qq!
select
s.source_name
from
$pid_schema.pw_source s,$pid_schema.pw_pathway p,
$pid_schema.pw_pathway_atom pa, $pid_schema.pw_edge e
where
(e.mol_id = $mol
or e.mol_id in (select family_mol_id from $pid_schema.pw_family_member
where member_mol_id = $mol))
and pa.atom_id = e.atom_id
and p.pathway_id = pa.pathway_id
and p.pathway_source_id = s.source_id
!;
$stm = $db->prepare($sql);
if(not $stm) {
return "prepare failed: $sql\n";
}
if(!$stm->execute()) {
print STDERR "execute failed: $sql\n";
return;
}
while (( my $s ) = $stm->fetchrow_array()) {
$s =~ s/NATURE/NCI-Nature curated/;
$s =~ s/BioCarta/BioCarta Imported/;
$source = $s;
}
for my $nametype (keys %{ $$mol2name{$mol} }) {
for my $name (keys %{ $$mol2name{$mol}{$nametype} }) {
push @names, $name;
}
}
if (($source eq 'NCI-Nature curated') || ($source eq 'BioCarta Imported')) {
push @lines, "<a href=\"" . MOLPAGE_URL($mol) . "\">" .
join(", ", @names, $source) . "</a><BR> ";
}
}
return join("<br>\n", @lines, "");
}
#############################################################
sub FindNamesForMols {
my ($db, $mols, $pid_schema) = @_;
my $mollist = join(",", keys %{ $mols });
my (%mol2name, %mol2ext_id);
my ($sql, $stm);
my ($molid, $extid, $id_type, $name_type, $name, $source);
$sql = qq!
select
e.mol_id,
e.id_type,
e.ext_mol_id
from
$pid_schema.pw_ext_mol_id e
where
e.mol_id in ($mollist)
!;
$stm = $db->prepare($sql);
if(not $stm) {
print STDERR "prepare failed: $sql\n";
return;
}
if(!$stm->execute()) {
print STDERR "execute failed: $sql\n";
return;
}
while (($molid, $id_type, $extid) = $stm->fetchrow_array()) {
$mol2ext_id{$molid}{$id_type}{$extid} = 1;
}
$sql = qq!
select
n.mol_id,
n.name_type,
n.mol_name
from
$pid_schema.pw_mol_name n
where
n.mol_id in ($mollist)
!;
$stm = $db->prepare($sql);
if(not $stm) {
print STDERR "prepare failed: $sql\n";
return;
}
if(!$stm->execute()) {
print STDERR "execute failed: $sql\n";
return;
}
while (($molid, $name_type, $name) = $stm->fetchrow_array()) {
$mol2name{$molid}{$name_type}{$name} = 1;
}
return (\%mol2name, \%mol2ext_id);
}
######################################################################
sub SearchPathwayKeywords_1 {
my ($base, $word, $format) = @_;
$BASE = $base;
my ($sql, $stm);
my ($source, $pname, $ext_id, $pid);
my (@lines);
$word =~ s/^\s+//;
$word =~ s/\s+$//;
$word =~ s/\s+/ /g;
$word = lc($word);
if ($format eq "html") {
return ListAllPathways_1($base, $word);
}
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";
die;
}
$sql = "select " .
"s.source_name, p.pathway_name, p.ext_pathway_id, p.pathway_id " .
"from $schema.pw_source s, $schema.pw_pathway p " .
"where s.source_id = p.pathway_source_id " .
"order by s.source_name, p.pathway_name";
$stm = $db->prepare($sql);
if(not $stm) {
print STDERR "$sql\n";
print STDERR "$DBI::errstr\n";
print STDERR "prepare call failed\n";
die;
}
if(!$stm->execute()) {
print STDERR "$sql\n";
print STDERR "$DBI::errstr\n";
print STDERR "execute call failed\n";
die;
}
while (($source, $pname, $ext_id, $pid) =
$stm->fetchrow_array()) {
if ((index(lc($pname), $word) > -1) ||
(index(lc($ext_id), $word) > -1)) {
$source =~ s/NATURE/NCI-Nature curated/;
$source =~ s/BioCarta/BioCarta Imported/;
if ($format eq "text") {
push @lines, join("\t", $source, $pname, $ext_id, $pid);
} elsif ($format eq "html") {
}
}
}
$stm->finish();
$db->disconnect();
if (@lines) {
return join("\n", @lines, "");
} else {
return "";
}
}