", table({-width => '100%', -class => 'violet3'}, Tr({-align => 'center'}, td("
", h4("Search term: $name"),
hr({-align => 'left',
-size => '2',
-width => '80%'});
my $species = $cgi->param('species');
my $wild_card = $cgi->param('wild');
my $go_term = $cgi->param('go_term');
my $go_final = $cgi->param('go_final');
my $dbh = connect_to_DB('mysql', 'S_pombe_YOGY_1', 'webdbsrv',
'3306', '', 'yogyro', '');
#test_query($dbh);
my $species_id = $species_id{$species};
my $tax_id = $species_tax_rev{$species_id};
my $new_name = lc $name;
# Is it a UniProt ID?
if ($name =~ /^([OPQ][\d][A-Z\d]{3}\d)/i) {
$uni_query = $name;
my $tmp_id = '';
if ($species eq 'S._pombe') {
$tmp_id = get_pombe_id_from_uni($dbh, $uni_query);
} elsif ($species eq 'C._elegans') {
$tmp_id = get_worm_id_from_uni($dbh, $uni_query);
} elsif ($species eq 'M._musculus') {
$tmp_id = get_mouse_id_from_uni($dbh, $uni_query);
} elsif ($species eq 'R._norvegicus') {
$tmp_id = get_rat_id_from_uni($dbh, $uni_query);
} elsif ($species eq 'H._sapiens') {
$tmp_id = get_ens_from_uni($dbh, $uni_query, $species_id);
} elsif ($species eq 'E.coli') {
$tmp_id = get_eco_id_from_uni($dbh, $uni_query);
}
if (not defined $tmp_id or not $tmp_id) {
$tmp_id = get_yogy_id($dbh, $uni_query);
}
$new_name = $tmp_id
if defined $tmp_id and $tmp_id;
#print "UNI: [$uni_query] [$new_name]\n";
}
# Is it a GI number?
if ($name =~ /^(HsM?|GI:)?(\d+)$/) {
$new_name = $2;
my $tmp_id = get_id_from_gi($dbh, $new_name, $tax_id);
if (defined $tmp_id and $tmp_id) {
$gi_query = $name;
$new_name = $tmp_id;
my $tmp_id = get_ens_from_gi($dbh, $gi_query, $species_id);
$ens_query = $tmp_id
if defined $tmp_id and $tmp_id;
#get_ipi_info_from_gi($dbh, $new_name, $tax_id);
}
}
#print "[$ens_query]\n";
undef my $gene_info;
# Is it an ENSEMBL ID?
if ( ($name =~ /^ENS/ or
$new_name =~ /^ENS/) and
($species eq 'H._sapiens' or
$species eq 'M._musculus' or
$species eq 'R._norvegicus') ) {
if ($name =~ /^ENS/) {
$ens_query = $name;
} elsif ($new_name =~ /^ENS/) {
$ens_query = $new_name;
}
$gene_info = get_info_from_ens($dbh, $ens_query, $species_id);
$gi_query = $gene_info->[1];
$uni_query = $gene_info->[5];
my $yogy_id = get_yogy_id($dbh, $gi_query);
my $gene_id = get_id_from_gi($dbh, $gi_query, $tax_id);
my $tmp_id = '';
if ($species_id == 130) {
$tmp_id = get_mouse_id($dbh, $gene_id);
} elsif ($species_id == 150) {
$tmp_id = get_rat_id($dbh, $gene_id);
}
if ($tmp_id) {
$new_name = $tmp_id;
}
if ($species eq 'M._musculus' or $species eq 'R._norvegicus') {
my $gene_info_new = get_gene_info($dbh, $new_name, $wild_card, $species);
$gene_info = $gene_info_new
if defined $gene_info_new and defined $gene_info_new->[0];
}
#print "[$new_name] [$yogy_id] [$gene_id]\n";
} else {
if ($species eq 'M._musculus') {
$new_name =~ s/^MGI://i;
} elsif ($species eq 'R._norvegicus') {
$new_name =~ s/^RGD://i;
}
$gene_info = get_gene_info($dbh, $new_name, $wild_card, $species);
my @ens_query = get_ens_from_ids($dbh, $name, $species_id);
if (scalar @ens_query > 1) {
print
'There are multiple Ensembl IDs for this gene: ';
my $pflag = 1;
foreach my $eid (@ens_query) {
if ($pflag == 1) {
$pflag = 0;
} else {
print ', ';
}
my $href = "http://www.sanger.ac.uk/cgi-bin/PostGenomics/S_pombe/YOGY/yogy-search.pl?gene=${eid}&species=${species}&wild=${wild_card}&go_term=${go_term}&go_final=${go_final}";
print "$eid";
}
print '.'
}
$ens_query = $ens_query[0]
if scalar @ens_query >= 1;
if (not $ens_query) {
my $tmp_id = get_gi_from_id($dbh, $gene_info->[1], $tax_id);
#print "[TMP: $tmp_id]\n";
my $tmp_id2 = get_ens_from_gi($dbh, $tmp_id, $species_id)
if defined $tmp_id and $tmp_id;
$ens_query = $tmp_id2
if defined $tmp_id2 and $tmp_id2;
}
if ($ens_query and not $gene_info->[0]) {
$gene_info = get_info_from_ens($dbh, $ens_query[0], $species_id);
}
#print "[$ens_query] [$name] [$species_id]\n";
}
#print Dumper $gene_info;
if (not defined $gene_info or not defined $gene_info->[0]) {
if ($wild_card eq 'Yes') {
print
"There are no gene IDs or names that include '$name'.
",
"You can try to search again below.
";
} elsif ($wild_card eq 'No') {
print
"'$name' is not recognised as a gene ID or name.
",
"You can search again below or try with the wild-card search option.
";
}
disconnect_from_DB($dbh);
print_help_bar();
print_form();
print_web_bar();
exit -1;
}
if (scalar @{$gene_info} == 1 and
($new_name eq lc($gene_info->[0][0]) or
$new_name eq lc($gene_info->[0][1]) ) ) {
$wild_card = 'No';
($gene_info) = get_gene_info($dbh, $new_name, $wild_card, $species);
}
$uni_query = $gene_info->[5]
if not defined $uni_query and not $uni_query;
if ($wild_card eq 'Yes') {
my @wildheadings = ('Result', 'Systematic ID', 'Primary name', 'Description');
foreach my $wh (@wildheadings) {
$wh = '' . $wh . '';
}
my @wildrows = td(\@wildheadings);
my $count = 1;
foreach my $nr (@{$gene_info}) {
my $new_id = make_gene_id($nr->[0]);
my $descrip = $nr->[2];
if ($species eq 'C._elegans') {
$descrip = $nr->[4]
if not $descrip;
}
my $script_name = $ENV{SCRIPT_NAME};
$script_name =~ s/\/\//\//g;
my $href =
"${script_name}?gene=$new_id&wild=No&species=$species&go_term=$go_term&go_final=$go_final";
push(@wildrows, td({-class => 'violet1',
-align => 'center'},
[$count,
a({-href => $href,
-style => $gStyle},
$new_id),
$nr->[1],
$descrip
]) );
$count++;
}
print ' ' x 2048;
print "
", table({-class => 'violet3', -cellpadding => '2'}, Tr(\@wildrows) ), "
"; print hr({-align => 'left', -size => '2', -width => '80%'}); } elsif ($wild_card eq 'No') { my $new_id = $gene_info->[0]; if ($species eq 'S._pombe') { $new_id = make_gene_id($new_id); } elsif ($species eq 'S._cerevisiae') { $new_id = make_gene_id($gene_info->[3]); } print "", a({-name => 'gene', -style => $gNone}, h4('Gene summary: ') ), "
"; print ' ' x 2048; print "| "; my @data_check = do_summary($dbh, $new_id, $species, $go_term, $go_final, $gene_info); print " | "; print_form(); print " |
" .
"" .
"
" .
"" .
"
"
]) );
}
my $kog_href = "http://www.ncbi.nlm.nih.gov/COG/new/";
my $inp_href = "http://inparanoid.cgb.ki.se/";
my $hom_href = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=homologene";
my $ort_href = "http://orthomcl.cbil.upenn.edu/";
my $gdb_href = "http://www.sanger.ac.uk/Projects/S_pombe/";
my $yes_img = '/PostGenomics/S_pombe/YOGY/images/green_y.jpg';
my $no_img = '/PostGenomics/S_pombe/YOGY/images/red_n.jpg';
my $img1 = '';
if ($data_check[0] eq 'Y') {
$img1 = "| " . "KOGs | $img1 |
| Inparanoid | $img2 |
| HomoloGene | $img3 |
| OrthoMCL | $img4 |
| Curated | $img5 |
", table({-width => '80%', -cellpadding => '2', -bgcolor => $species_colour{$species_id} }, Tr(\@namerows) ), "
"; return @data_check; } ############################################################################### sub do_kogs { my ($dbh, $new_id, $species, $go_term, $go_final, $gene_info) = @_; my $search_kog = $new_id; my $spec_id = $species_id{$species}; if ($species eq 'C._elegans') { $search_kog = $gene_info->[0] if defined $gene_info->[0] and $gene_info->[0]; } elsif ($species eq 'A._thaliana') { $search_kog =~ s/\.\d+$//; } elsif ($species eq 'D._melanogaster' or $species eq 'H._sapiens') { $search_kog = $gi_query; my $tax_id = $species_tax_rev{$spec_id}; my $tmp_id = get_gi_from_id($dbh, $search_kog, $tax_id); if (defined $tmp_id and $tmp_id) { $search_kog = $tmp_id; } else { $tmp_id = get_gi_from_id($dbh, $gene_info->[1], $tax_id); if (defined $tmp_id and $tmp_id ) { $search_kog = $tmp_id; } else { $tmp_id = get_gi_from_id($dbh, $gene_info->[3], $tax_id); $search_kog = $tmp_id if defined $tmp_id and $tmp_id; } } } my @kog_details = get_kogs_results($dbh, $search_kog, $spec_id); my @protein_id = get_prot_results($dbh, $kog_details[0]); my @kog_olc = split '', $kog_details[1]; undef my $func_details; foreach my $ko (@kog_olc) { my @func_details = get_func_results($dbh, $ko); my $href1 = "/PostGenomics/S_pombe/YOGY/function.shtml"; my $href2 = "http://www.ncbi.nlm.nih.gov/COG/grace/shokog.cgi?fun=$ko"; $func_details .= "" . $ko . "", a({-name => 'kog', -style => $gNone}, h4('KOG results: ') ), "
"; undef my @kog; push @kog, @kogheadings; push @kog, @kogrows; print ' ' x 2048; print "", table({-class => 'violet3', -cellpadding => '2', -bgcolor => $kog_colour}, Tr(\@kog) ), "
"; undef my @kog2; push @kog2, @kogheadings2; push @kog2, @kogrows2; print ' ' x 2048; print "", table({-class => 'violet3', -cellpadding => '2', -width => '60%', -bgcolor => $kog_colour}, Tr(\@kog2) ), "
"; undef my @kog3; push @kog3, @orthheadings; push @kog3, @orthrows; print ' ' x 2048; print "", table({-class => 'violet3', -cellpadding => '2'}, Tr(\@kog3) ), "
"; if ($go_final eq 'No' and $go_term eq 'Yes') { print_go_table($dbh, 'KOG', $local_search_gos); } print_back_to_top(); } ############################################################################### sub do_inparanoid { my ($dbh, $new_id, $species, $go_term, $go_final, $gene_info) = @_; my $search_inp = $new_id; if ($species eq 'S._cerevisiae') { $search_inp = $gene_info->[0]; } elsif ($species eq 'A._thaliana') { $search_inp = $gene_info->[1]; $search_inp =~ s/\.\d+$//; } elsif ($species eq 'C._elegans') { $search_inp = $gene_info->[3]; } elsif ($species eq 'H._sapiens') { $search_inp = $ens_query; } elsif ($species eq 'E._coli') { my $tmp_id = get_eco_ref_acc($dbh, $gene_info->[0]); $search_inp = $tmp_id, $search_inp =~ s/\.\d+$// if defined $tmp_id and $tmp_id; } my @inparanoid_results = get_inparanoid_results($dbh, $search_inp, $species); # Selected organisms for Inparanoid. my @inpara_keys = qw(ensAG ensCF ensDR ensFR ensGG ensHS ensMM ensPT ensRN modCE modDD modDM modMM modOG modRR modSC modSP ncbAT ncbEC sanPF); # Not in KOGs or Homologene - so exclude. my @inpara_keys_excl = qw(ensAM ensCE ensDM ensTN modCB modDP); undef my @inpara_keys2; foreach my $inkey (@inpara_keys) { if ($inkey eq 'ensMM') { push @inpara_keys2, 'EMM'; } elsif ($inkey eq 'ensRN') { push @inpara_keys2, 'ERN'; } else { push @inpara_keys2, $species_3let{$inparanoid_species{$inkey} }; } } undef my @inpara; undef my @prot_ids; undef my $ortholog_count; undef my $species_count; undef my %inparanoid_count; undef my $local_search_gos; my $search_db = ''; PROT: foreach my $prot (@inparanoid_results) { #print "[$species_tax_rev{$inparanoid_species{$prot->[2]} }]\n"; my $species_id = $inparanoid_species{$prot->[2]}; my $search_id = $prot->[5]; my $key_flag = 0; foreach my $key (@inpara_keys) { $key_flag = 1 if $key eq $prot->[2]; } next if $key_flag == 0; foreach my $excl (@inpara_keys_excl) { if ($excl eq $prot->[3]) { next PROT; } } my $pid_flag = 0; PID: foreach my $pid (@prot_ids) { if ($search_id eq $pid) { $pid_flag = 1; last PID; } } if ($pid_flag == 0) { $inparanoid_count{$prot->[2]}++; } if ($species_id eq $species_id{$species}) { push @prot_ids, $search_id; } my $uni_id = ''; my $href = ''; my $title = ''; my $gene_name = ''; if ($prot->[2] =~ /^ens/) { $href = "http://dec2004.archive.ensembl.org/$ensembl_species{$species_id}/protview?peptide=$search_id"; $title = 'Ensembl'; my $gene_info = get_info_from_ens($dbh, $search_id, $species_id); $uni_id = $gene_info->[5]; $gene_name = get_name_from_ens($dbh, $search_id, $species_id); if ($prot->[2] eq 'ensMM' or $prot->[2] eq 'ensRN') { $gene_name = (split /,/, $gene_name)[0]; $search_id = $gene_name if defined $gene_name and $gene_name; } else { $gene_name = (split /,/, $gene_name)[1]; } } elsif ($prot->[2] =~ /^swt/) { $href = "http://us.expasy.org/cgi-bin/niceprot.pl?$search_id"; $title = 'UniProt'; } elsif ($prot->[2] eq 'sanPF') { $href = "http://www.genedb.org/genedb/Search?organism=malaria&name=$search_id"; $title = 'GeneDB'; } elsif ($prot->[2] eq 'ncbEC') { $href = "http://ecogene.org/geneinfo.php?eg_id=$search_id"; $title = 'EcoGene'; $uni_id = get_eco_uni_id($dbh, $search_id); } elsif ($prot->[2] =~ /^ncb/) { my $tax_id = $species_tax_rev{$species_id}; $href = "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?list_uids=$search_id"; $title = 'NCBI'; my $prot_id = get_prot_id($dbh, $search_id, $tax_id); $uni_id = get_uniprot_id2($dbh, $prot_id, $tax_id); } elsif ($prot->[2] eq 'modCB' or $prot->[2] eq 'modCE') { my $tmp_id = get_worm_pid($dbh, $search_id); if ($tmp_id) { $search_id = $tmp_id; } $href = "http://www.wormbase.org/db/gene/gene?name=$search_id"; $title = 'WormBase'; $uni_id = get_worm_uni_id($dbh, $search_id); } elsif ($prot->[2] eq 'modSP') { $href = "http://www.genedb.org/genedb/Search?organism=S.+pombe&name=$search_id"; $title = 'GeneDB'; $uni_id = get_pombe_uni_id($dbh, $search_id); } elsif ($prot->[2] eq 'modSC') { $href = "http://db.yeastgenome.org/cgi-bin/locus.pl?locus=$search_id"; $title = 'SGD'; } elsif ($prot->[2] eq 'modDD') { $href = "http://dictybase.org/db/cgi-bin/gene_page.pl?dictybaseid=$search_id"; $title = 'dictyBase'; } elsif ($prot->[2] eq 'modDM') { $href = "http://flybase.net/cgi-bin/fbidq.html?$search_id"; $title = 'FlyBase'; } elsif ($prot->[2] eq 'modDP') { $href = "http://flybase.net/cgi-bin/gbrowse_fb/dpse?id=$search_id"; $title = 'FlyBase'; } elsif ($prot->[2] eq 'modMM') { $href = "http://www.informatics.jax.org/searches/accession_report.cgi?id=MGI:$search_id"; $title = 'MGI'; $uni_id = get_mouse_uni_id($dbh, $search_id); } elsif ($prot->[2] eq 'modOG') { $href = "http://www.gramene.org/db/protein/protein_search?acc=$search_id"; $title = 'Gramene'; $uni_id = $search_id; } elsif ($prot->[2] eq 'modRR') { $href = "http://rgd.mcw.edu/tools/genes/genes_view.cgi?id=$search_id"; $title = 'RGD'; $uni_id = get_rat_uni_id($dbh, $search_id); } my $tmp_id = ''; if ($prot->[2] eq 'modDM') { ($tmp_id = $search_id) =~ s/\-(\S+)$//; $tmp_id = get_fly_id($dbh, $tmp_id); } elsif ($prot->[2] eq 'ncbAT') { $tmp_id = get_arab_id($dbh, $search_id); } if ($tmp_id) { $search_id = $tmp_id; } if ($prot->[0] eq 'query') { if (not defined $uni_id and not $uni_id) { $uni_id = $uni_query if defined $uni_query and $uni_query; } $search_db = $prot->[2]; } if ($go_term eq 'Yes') { my $search_go = $search_id; if ($prot->[2] eq 'modMM') { $search_go = 'MGI:' . $search_go; } elsif ($prot->[2] eq 'modRR') { $search_go = 'RGD:' . $search_go; } my $uni_go_id = $uni_id; $uni_go_id =~ s/\-\d+$//; $local_search_gos = search_go_with_ids($dbh, $search_go, $uni_go_id, $species_id, $local_search_gos); } if ($prot->[5] ne $search_id) { $search_id = $prot->[5] . '", a({-name => 'inparanoid', -style => $gNone}, h4('Inparanoid results: ') ), "
", "Selected databases only", table({-class => 'violet3', -cellpadding => '2'}, Tr(\@inparanoidheadings) ), "
"; undef my @inparanoidheadings2; push(@inparanoidheadings2, td({-align => 'center', -style => 'font-style: italic'}, ['Species', 'Link to cluster', 'Score', 'Model organism", table({-class => 'violet3', -cellpadding => '2'}, Tr(\@inparanoid) ), "
"; if ($go_final eq 'No' and $go_term eq 'Yes') { print_go_table($dbh, 'Inparanoid', $local_search_gos); } print_back_to_top(); } ############################################################################### sub do_homologene { my ($dbh, $new_id, $species, $go_term, $go_final, $gene_info) = @_; my $search_hom = $gene_info->[1]; my @homologene_results = get_homologene_results($dbh, $new_id, $search_hom, $species); my @homologene_keys = qw(Hsa Ptr Cfa Mmu Rno Gga Dme Aga Cel Spo Sce Kla Ego Mgr Ncr Ath Osa Pfa); my @homologene_keys_excl = qw(); undef my %homologene_count_hash; undef my @homologene; undef my @hom; my $HID = ''; undef my $local_search_gos; #print "[@homologene_results]\n"; PROT: foreach my $prot (@homologene_results) { $HID = $prot->[0]; my $species_id = $species_tax{$prot->[1]}; my $species_tlc = $species_3let{$species_id}; my $search_id = $prot->[3]; my $gi = $prot->[4]; my $key_flag = 0; foreach my $key (@homologene_keys) { $key_flag = 1 if $key eq $species_tlc; } next if $key_flag == 0; foreach my $excl (@homologene_keys_excl) { if ($excl eq $species_tlc) { next PROT; } } $homologene_count_hash{$species_tlc}++; my $tmp_id = ''; if ($species_id == 20) { $tmp_id = get_worm_pid($dbh, $search_id); } elsif ($species_id == 30) { $tmp_id = get_fly_id($dbh, $search_id); } elsif ($species_id == 50) { $tmp_id = get_budding_id($dbh, $search_id); } elsif ($species_id == 60) { $tmp_id = make_gene_id(get_pombe_id($dbh, $search_id) ); } elsif ($species_id == 130) { $tmp_id = get_mouse_id($dbh, $search_id); } elsif ($species_id == 150) { $tmp_id = get_rat_id($dbh, $search_id); } if ($tmp_id) { $search_id = $tmp_id; } my $uni_id = get_uniprot_id2($dbh, $gi, $species_tax_rev2{$species_id}); my $tmp_uni_id = ''; if ($species_id == 60) { $tmp_uni_id = get_pombe_uni_id($dbh, $search_id); } elsif ($species_id == 130) { $tmp_uni_id = get_mouse_uni_id($dbh, $search_id); } elsif ($species_id == 150) { $tmp_uni_id = get_rat_uni_id($dbh, $search_id); } elsif ($species_id == 20) { $tmp_uni_id = get_worm_uni_id($dbh, $search_id); } if ($tmp_uni_id) { $uni_id = $tmp_uni_id; } if ($go_term eq 'Yes') { my $search_go = $search_id; if ($species_id == 130) { $search_go = 'MGI:' . $search_go; } elsif ($species_id == 150) { $search_go = 'RGD:' . $search_go; } my $uni_go_id = $uni_id; $uni_go_id =~ s/\-\d+$//; $local_search_gos = search_go_with_ids($dbh, $search_go, $uni_go_id, $species_id, $local_search_gos); } my $href = "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&val=$prot->[4]"; my $href2 = "http://www.expasy.org/cgi-bin/niceprot.pl?$uni_id"; $tmp_id = ''; if ($species_id == 20) { $tmp_id = get_worm_gid($dbh, $search_id); if ($tmp_id) { if ($search_id and $prot->[3] !~ /^CE/) { $search_id = $search_id . ';", a({-name => 'homologene', -style => $gNone}, h4('HomoloGene results: ') ), "
"; my $graph = draw_homologene_graph(\@homologene_keys, \@homologene_values); #my $graph = ''; my $href = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=homologene&dopt=Homologene&list_uids=$HID"; undef my @hom; push(@hom, td({-align => 'center', -style => 'font-style: italic'}, ['HomoloGene cluster', 'Phylogenetic pattern']) ); push(@hom, td({-align => 'center'}, [a({-href => $href, -style => $gStyle, -target => $gBlank, -title => 'HomoloGene cluster page'}, $HID), "", table({-class => 'violet3', -cellpadding => '2'}, Tr(\@hom) ), "
"; undef my @hom2; push(@hom2, td({-align => 'center', -style => 'font-style: italic'}, ['Species', 'Gene ID', 'NCBI link', 'UniProt link']) ); push @hom2, @homologene; print ' ' x 2048; print "", table({-class => 'violet3', -cellpadding => '2'}, Tr(\@hom2) ), "
"; if ($go_final eq 'No' and $go_term eq 'Yes') { print_go_table($dbh, 'Homologene', $local_search_gos); } print_back_to_top(); } ############################################################################### sub do_orthomcl { my ($dbh, $new_id, $species, $go_term, $go_final, $gene_info) = @_; my $search_orth = $new_id; if ($species eq 'S._cerevisiae') { $search_orth = $gene_info->[3]; } elsif ($species eq 'C._elegans') { my $tmp_id = get_worm_wid($dbh, $gene_info->[3]); if (defined $tmp_id and $tmp_id) { $search_orth = $tmp_id; } else { my $tmp_id = get_worm_wid2($dbh, $gene_info->[0]); $search_orth = $tmp_id if defined $tmp_id and $tmp_id; } } elsif ($species eq 'H._sapiens' or $species eq 'M._musculus' or $species eq 'R._norvegicus') { $search_orth = $ens_query; $search_orth = ' ' if not $search_orth; } elsif ($species eq 'E._coli') { my $tmp_id = get_eco_ref_gi($dbh, $gene_info->[0]); $search_orth = $tmp_id if defined $tmp_id and $tmp_id; } #print "[$search_orth]\n"; my $orthomcl_cluster = get_orthomcl_cluster($dbh, $search_orth, $species); my @orthomcl_results = get_orthomcl_results($dbh, $orthomcl_cluster); # Selected organisms for OrthoMCL. my @orthomcl_keys = qw(Aga Ago Ath Cel Cgl Cne Ddi Dha Dme Dre Eco Ecu Fru Gga Hsa Kla Mmu Ncr Osa Pfa Rno Sce Spo Yli); my @orthomcl_keys_excl = qw(Hal Mja Sso Neq Wsu Gsu Atu Rso Aae Tma Det Dra Tpa Cte Rba Cpn Syn Mtu Ban Ehi Cme Tps Tgo Cpa Cho Pyo Pkn The Cbr Cin Tni); undef my @ortho; undef my @oprot_ids; undef my %orthomcl_count_hash; undef my $local_search_gos; PROT: foreach my $prot (@orthomcl_results) { $prot->[1] = ucfirst $prot->[1]; my $species_id = $species_3let_rev{$prot->[1]}; my $search_id = $prot->[0]; my $key_flag = 0; foreach my $key (@orthomcl_keys) { $key_flag = 1 if $key eq $prot->[1]; } next if $key_flag == 0; foreach my $excl (@orthomcl_keys_excl) { if ($excl eq $prot->[1]) { next PROT; } } $orthomcl_count_hash{$prot->[1]}++; my $uni_id = ''; my $href = ''; my $title = ''; my $gene_name = ''; if ($prot->[1] eq 'Aga' or $prot->[1] eq 'Dre' or $prot->[1] eq 'Fru' or $prot->[1] eq 'Gga' or $prot->[1] eq 'Hsa' or $prot->[1] eq 'Mmu' or $prot->[1] eq 'Rno' or $prot->[1] eq 'Tni') { $href = "http://apr2005.archive.ensembl.org/$ensembl_species{$species_id}/protview?peptide=$search_id"; $title = 'Ensembl'; my $gene_info = get_info_from_ens($dbh, $search_id, $species_id); $uni_id = $gene_info->[5]; $gene_name = get_name_from_ens($dbh, $search_id, $species_id); if ($prot->[1] eq 'Mmu' or $prot->[1] eq 'Rno') { $gene_name = (split /,/, $gene_name)[0]; $search_id = $gene_name if defined $gene_name and $gene_name; } else { $gene_name = (split /,/, $gene_name)[1]; } } elsif ($prot->[1] eq 'Pfa') { $href = "http://www.genedb.org/genedb/Search?organism=malaria&name=$search_id"; $title = 'GeneDB'; } elsif ($prot->[1] eq 'Eco') { $href = "http://ecogene.org/geneinfo.php?eg_id=$search_id"; $title = 'EcoGene'; $uni_id = get_eco_uni_id($dbh, $search_id); } elsif ($prot->[1] eq 'Ecu') { my $tax_id = $species_tax_rev{$species_id}; $href = "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?list_uids=$search_id"; $title = 'NCBI'; (my $new_search_id = $search_id) =~ s/\.\d+$//; my $prot_id = get_prot_id($dbh, $new_search_id, $tax_id); $uni_id = get_uniprot_id2($dbh, $prot_id, $tax_id); } elsif ($prot->[1] eq 'Cel' or $prot->[1] eq 'Cbr') { my $tmp_id = get_worm_pid($dbh, $search_id); if ($tmp_id) { $search_id = $tmp_id; } $href = "http://www.wormbase.org/db/gene/gene?name=$search_id"; $title = 'WormBase'; $uni_id = get_worm_uni_id($dbh, $search_id); } elsif ($prot->[1] eq 'Spo') { $href = "http://www.genedb.org/genedb/Search?organism=S.+pombe&name=$search_id"; $title = 'GeneDB'; $uni_id = get_pombe_uni_id($dbh, $search_id); } elsif ($prot->[1] eq 'Sce') { $href = "http://db.yeastgenome.org/cgi-bin/locus.pl?locus=$search_id"; $title = 'SGD'; } elsif ($prot->[1] eq 'Ddi') { $href = "http://dictybase.org/db/cgi-bin/gene_page.pl?dictybaseid=$search_id"; $title = 'dictyBase'; } elsif ($prot->[1] eq 'Dme') { $href = "http://flybase.net/cgi-bin/fbidq.html?$search_id"; $title = 'FlyBase'; } elsif ($prot->[1] eq 'Osa') { #$href = "http://www.gramene.org/db/protein/protein_search?acc=$search_id"; #$title = 'Gramene'; } elsif ($prot->[1] eq 'Ath') { $href = "http://www.arabidopsis.org/servlets/TairObject?type=gene&name=$search_id"; $title = 'TAIR'; } elsif ($prot->[1] eq 'Ago' or $prot->[1] eq 'Cgl' or $prot->[1] eq 'Kla') { $href = "http://wolfe.gen.tcd.ie/cgi/browser/browser.pl?win=7&gene=$search_id"; $title = 'Yeast Gene Order Browser'; } elsif ($prot->[1] eq 'Cne') { $href = "http://www.genome.jp/dbget-bin/www_bget?cne:$search_id"; $title = 'KEGG'; } elsif ($prot->[1] eq 'Dha') { $href = "http://cbi.labri.fr/Genolevures/elt/DEHA/$search_id"; $title = 'Genolevures'; } elsif ($prot->[1] eq 'Yli') { $href = "http://cbi.labri.fr/Genolevures/elt/YALI/$search_id"; $title = 'Genolevures'; } my $tmp_id = ''; if ($prot->[1] eq 'Sce') { $tmp_id = uc(get_budding_id($dbh, $search_id) ); } elsif ($prot->[1] eq 'Dme') { ($tmp_id = $search_id) =~ s/\-(\S+)$//; $tmp_id = get_fly_id($dbh, $tmp_id); } elsif ($prot->[1] eq 'Ath') { $tmp_id = get_arab_id($dbh, $search_id); } elsif ($prot->[1] eq 'Cel') { $tmp_id = get_worm_pid2($dbh, $search_id); } if ($tmp_id) { $search_id = $tmp_id; } if ($go_term eq 'Yes') { my $search_go = $search_id; my $uni_go_id = $uni_id; $uni_go_id =~ s/\-\d+$//; $local_search_gos = search_go_with_ids($dbh, $search_go, $uni_go_id, $species_id, $local_search_gos); } if ($prot->[1] eq 'Cel') { if ($prot->[0] ne $search_id) { my $tmp_id = get_worm_gid($dbh, $search_id); $search_id = $prot->[0] . '", a({-name => 'orthomcl', -style => $gNone}, h4('OrthoMCL results: ') ), "
", "Selected databases only", table({-class => 'violet3', -cellpadding => '2'}, Tr(\@orthomclheadings) ), "
"; undef my @orthomclheadings2; push(@orthomclheadings2, td({-align => 'center', -style => 'font-style: italic'}, ['Species', 'OrthoMCL", table({-class => 'violet3', -cellpadding => '2'}, Tr(\@orthomcl) ), "
"; if ($go_final eq 'No' and $go_term eq 'Yes') { print_go_table($dbh, 'OrthoMCL', $local_search_gos); } print_back_to_top(); } ############################################################################### sub do_vals { my ($dbh, $new_id, $species, $go_term, $go_final, $gene_info) = @_; my @curated_results = get_val_results($dbh, $new_id); undef my @val_rows; undef my @val; push(@val_rows, td({-align => 'center', -style => 'font-style: italic'}, ['S. pombe", a({-name => 'curated', -style => $gNone}, h4('Curated yeast ortholog results: ') ), "
"; print ' ' x 2048; print "", table({-class => 'violet3', -cellpadding => '2'}, Tr(\@val_rows) ), "
"; if ($go_final eq 'No' and $go_term eq 'Yes') { print_go_table($dbh, 'curated homolog', $local_search_gos); } print_back_to_top(); } ############################################################################### sub print_help_bar { print table({-width => '100%', -cellpadding => '2'}, Tr({-align => 'center', -valign => 'top', -class => 'violet3'}, [td(['', 'YOGY Home", '', 'YOGY Help", '']) ]) ); } ############################################################################### sub print_web_bar { print table({-width => '100%', -cellpadding => '2'}, Tr({-align => 'center', -valign => 'top', -class => 'violet3'}, [td(['', 'webmaster@sanger.ac.uk', '']) ]) ); } ############################################################################### sub print_form { print start_form(); print p('Search for gene by ID or name: ', textfield('gene', '', 30, 100) ); print p('Query species: ', scrolling_list(-name => 'species', -values => ['A._thaliana', 'C._elegans', 'D._discoideum', 'D._melanogaster', 'E._coli', 'H._sapiens', 'M._musculus', 'P._falciparum', 'R._norvegicus', 'S._cerevisiae', 'S._pombe'], -labels => {'A._thaliana' => 'A. thaliana', 'C._elegans' => 'C. elegans', 'D._discoideum' => 'D. discoideum', 'D._melanogaster' => 'D. melanogaster', 'E._coli' => 'E. coli', 'H._sapiens' => 'H. sapiens', 'M._musculus' => 'M. musculus', 'P._falciparum' => 'P. falciparum', 'R._norvegicus' => 'R. norvegicus', 'S._cerevisiae' => 'S. cerevisiae', 'S._pombe' => 'S. pombe'}, -size => 1, -default => 'S._pombe') ); print p('Include wild-cards: ', radio_group(-name => 'wild', -values => ['Yes', 'No'], -default => 'No') ); print p('Search for GO info: ', radio_group(-name => 'go_term', -values => ['Yes', 'No'], -default => 'No') ); print p('GO info in one table: ', radio_group(-name => 'go_final', -values => ['Yes', 'No'], -default => 'Yes') ); print p(submit('Find orthologs'), defaults('Reset') ); print ' ' x 2048; print end_form(); } ############################################################################### sub print_back_to_top { print a({-href => "#gene", -style => $gNone}, 'Back to the top'); print hr({-align => 'left', -size => '2', -width => '80%'}); } ############################################################################### sub get_gene_info { my ($dbh, $gene_name, $wild_card, $species) = @_; my $gene_info = undef; if ($species eq 'S._pombe') { if ($wild_card eq 'No') { $gene_info = get_gene_info_pombe($dbh, $gene_name); } elsif ($wild_card eq 'Yes') { $gene_info = get_gene_info_pombe_wild($dbh, $gene_name); } } elsif ($species eq 'S._cerevisiae') { if ($wild_card eq 'No') { $gene_info = get_gene_info_budding($dbh, $gene_name); } elsif ($wild_card eq 'Yes') { $gene_info = get_gene_info_budding_wild($dbh, $gene_name); } } elsif ($species eq 'C._elegans') { if ($wild_card eq 'No') { $gene_info = get_gene_info_worm($dbh, $gene_name); } elsif ($wild_card eq 'Yes') { $gene_info = get_gene_info_worm_wild($dbh, $gene_name); } } elsif ($species eq 'A._thaliana') { if ($wild_card eq 'No') { $gene_info = get_gene_info_arab($dbh, $gene_name); } elsif ($wild_card eq 'Yes') { $gene_info = get_gene_info_arab_wild($dbh, $gene_name); } } elsif ($species eq 'D._melanogaster') { if ($wild_card eq 'No') { $gene_info = get_gene_info_fly($dbh, $gene_name); } elsif ($wild_card eq 'Yes') { $gene_info = get_gene_info_fly_wild($dbh, $gene_name); } } elsif ($species eq 'H._sapiens') { if ($wild_card eq 'No') { $gene_info = get_gene_info_human($dbh, $gene_name); } elsif ($wild_card eq 'Yes') { $gene_info = get_gene_info_human_wild($dbh, $gene_name); } } elsif ($species eq 'M._musculus') { if ($wild_card eq 'No') { $gene_info = get_gene_info_mouse($dbh, $gene_name); } elsif ($wild_card eq 'Yes') { $gene_info = get_gene_info_mouse_wild($dbh, $gene_name); } } elsif ($species eq 'R._norvegicus') { if ($wild_card eq 'No') { $gene_info = get_gene_info_rat($dbh, $gene_name); } elsif ($wild_card eq 'Yes') { $gene_info = get_gene_info_rat_wild($dbh, $gene_name); } } elsif ($species eq 'P._falciparum') { if ($wild_card eq 'No') { $gene_info = get_gene_info_plasmo($dbh, $gene_name); } elsif ($wild_card eq 'Yes') { $gene_info = get_gene_info_plasmo_wild($dbh, $gene_name); } } elsif ($species eq 'D._discoideum') { if ($wild_card eq 'No') { $gene_info = get_gene_info_dicty($dbh, $gene_name); } elsif ($wild_card eq 'Yes') { $gene_info = get_gene_info_dicty_wild($dbh, $gene_name); } } elsif ($species eq 'E._coli') { if ($wild_card eq 'No') { $gene_info = get_gene_info_eco($dbh, $gene_name); } elsif ($wild_card eq 'Yes') { $gene_info = get_gene_info_eco_wild($dbh, $gene_name); } } return ($gene_info); } ############################################################################### sub get_gene_info_pombe { my ($dbh, $gene_name) = @_; my $gene_info = undef; my $string = qq(SELECT * FROM pombe_gene WHERE GeneDB_systematic_id = ? OR GeneDB_primary = ? OR PombePD_Systematic = ?); my $sth_querya = $dbh->prepare($string); $sth_querya->execute($gene_name, $gene_name, $gene_name); $gene_info = $sth_querya->fetchrow_arrayref(); if (not defined $gene_info) { my $string = qq(SELECT protein_id FROM pombe_synonyms WHERE synonym = ?); my $sth_queryb = $dbh->prepare($string); $sth_queryb->execute($gene_name); $gene_info = $sth_queryb->fetchrow_arrayref(); if (defined $gene_info) { my $string = qq(SELECT * FROM pombe_gene WHERE GeneDB_systematic_id = ?); my $sth_queryc = $dbh->prepare($string); $sth_queryc->execute($gene_info->[0]); $gene_info = $sth_queryc->fetchrow_arrayref(); } } return $gene_info; } ############################################################################### sub get_gene_info_pombe_wild { my ($dbh, $gene_name) = @_; my $gene_info = undef; my $string = qq(SELECT * FROM pombe_gene WHERE GeneDB_systematic_id LIKE ? OR GeneDB_primary LIKE ? OR PombePD_Systematic LIKE ? LIMIT 0, 100); my $sth_querya = $dbh->prepare($string); $sth_querya->execute('%' . $gene_name . '%', '%' . $gene_name . '%', '%' . $gene_name . '%'); while (my @row = $sth_querya->fetchrow_array() ) { push @{$gene_info}, \@row; } if (not defined $gene_info) { my $string = qq(SELECT protein_id FROM pombe_synonyms WHERE synonym LIKE ?); my $sth_queryb = $dbh->prepare($string); $sth_queryb->execute('%' . $gene_name . '%'); while (my @row = $sth_queryb->fetchrow_array() ) { push @{$gene_info}, \@row; } if (defined $gene_info) { foreach my $qu (@{$gene_info}) { my $string = qq(SELECT * FROM pombe_gene WHERE GeneDB_systematic_id = ? LIMIT 0, 100); my $sth_queryc = $dbh->prepare($string); $sth_queryc->execute($qu); my @row = $sth_queryc->fetchrow_array(); push @{$gene_info}, \@row; } } } return $gene_info; } ############################################################################### sub get_gene_info_budding { my ($dbh, $gene_name) = @_; my $gene_info = undef; my $string = qq(SELECT SGDID, SGD_symbol, SGD_descrip, SGD_sys_name FROM budding_gene WHERE SGD_symbol = ? OR SGD_sys_name = ? OR SGDID = ?); my $sth_query = $dbh->prepare($string); $sth_query->execute($gene_name, $gene_name, $gene_name); $gene_info = $sth_query->fetchrow_arrayref(); return $gene_info; } ############################################################################### sub get_gene_info_budding_wild { my ($dbh, $gene_name) = @_; my $gene_info = undef; my $string = qq(SELECT SGDID, SGD_symbol, SGD_descrip, SGD_sys_name FROM budding_gene WHERE SGD_symbol LIKE ? OR SGD_sys_name LIKE ? OR SGDID LIKE ? LIMIT 0, 100); my $sth_query = $dbh->prepare($string); $sth_query->execute('%' . $gene_name . '%', '%' . $gene_name . '%', '%' . $gene_name . '%'); while (my @row = $sth_query->fetchrow_array() ) { push @{$gene_info}, \@row; } return $gene_info; } ############################################################################### sub get_gene_info_worm { my ($dbh, $gene_name) = @_; my $gene_info = undef; my $string = qq(SELECT WP.WP_id, WG.WB_name, WP.CE_descrip, WG.WB_id, WG.WB_descrip FROM worm_gene WG, worm_pep WP WHERE WG.CE_id = WP.CE_id AND (WP.WP_id = ? OR WG.WB_name = ? OR WG.WB_id = ? OR WG.CE_id = ?) ); my $sth_query = $dbh->prepare($string); $sth_query->execute('WP:' . $gene_name, $gene_name, $gene_name, $gene_name); $gene_info = $sth_query->fetchrow_arrayref(); if (not $gene_info->[0]) { my $string = qq(SELECT WP_id, CE_id, CE_descrip FROM worm_pep WHERE WP_id = ? OR CE_id = ?); my $sth_query = $dbh->prepare($string); $sth_query->execute('WP:' . $gene_name, $gene_name); $gene_info = $sth_query->fetchrow_arrayref(); } $gene_info->[0] =~ s/^WP://; return $gene_info; } ############################################################################### sub get_gene_info_worm_wild { my ($dbh, $gene_name) = @_; my $gene_info = undef; my $string = qq(SELECT WP.WP_id, WG.WB_name, WP.CE_descrip, WG.WB_id, WG.WB_descrip FROM worm_gene WG, worm_pep WP WHERE WG.CE_id = WP.CE_id AND (WP.WP_id LIKE ? OR WG.WB_name LIKE ? OR WG.WB_id LIKE ? OR WG.CE_id LIKE ?) LIMIT 0, 100); my $sth_query = $dbh->prepare($string); $sth_query->execute('%' . $gene_name . '%', '%' . $gene_name . '%', '%' . $gene_name . '%', '%' . $gene_name . '%'); while (my @row = $sth_query->fetchrow_array() ) { $row[0] =~ s/^WP://; push @{$gene_info}, \@row; } return $gene_info; } ############################################################################### sub get_gene_info_fly { my ($dbh, $gene_name) = @_; my $gene_info = undef; my $string = qq(SELECT DM_id, FB_name, FB_descrip, FB_id FROM fly_gene WHERE DM_id = ? OR FB_name = ? OR FB_id = ?); my $sth_query = $dbh->prepare($string); $sth_query->execute($gene_name, $gene_name, $gene_name); $gene_info = $sth_query->fetchrow_arrayref(); return $gene_info; } ############################################################################### sub get_gene_info_fly_wild { my ($dbh, $gene_name) = @_; my $gene_info = undef; my $string = qq(SELECT DM_id, FB_name, FB_descrip, FB_id FROM fly_gene WHERE DM_id LIKE ? OR FB_name LIKE ? OR FB_id LIKE ? LIMIT 0, 100); my $sth_query = $dbh->prepare($string); $sth_query->execute('%' . $gene_name . '%', '%' . $gene_name . '%', '%' . $gene_name . '%'); while (my @row = $sth_query->fetchrow_array() ) { push @{$gene_info}, \@row; } return $gene_info; } ############################################################################### sub get_gene_info_arab { my ($dbh, $gene_name) = @_; my $gene_info = undef; my $string = qq(SELECT TAIR_id, prot_acc, prot_gi FROM arab_gene WHERE TAIR_id LIKE ? OR prot_acc LIKE ? OR prot_gi = ?); my $sth_query = $dbh->prepare($string); $sth_query->execute($gene_name . '%', $gene_name . '%', $gene_name); $gene_info = $sth_query->fetchrow_arrayref(); return $gene_info; } ############################################################################### sub get_gene_info_arab_wild { my ($dbh, $gene_name) = @_; my $gene_info = undef; my $string = qq(SELECT TAIR_id, prot_acc, prot_gi FROM arab_gene WHERE TAIR_id LIKE ? OR prot_acc LIKE ? OR prot_gi LIKE ? LIMIT 0, 100); my $sth_query = $dbh->prepare($string); $sth_query->execute('%' . $gene_name . '%', '%' . $gene_name . '%', '%' . $gene_name . '%'); while (my @row = $sth_query->fetchrow_array() ) { push @{$gene_info}, \@row; } return $gene_info; } ############################################################################### sub get_gene_info_human { my ($dbh, $gene_name) = @_; my $gene_info = undef; my $string = qq(SELECT human_id, human_id FROM human_gene WHERE human_id = ?); my $sth_query = $dbh->prepare($string); $sth_query->execute($gene_name); $gene_info = $sth_query->fetchrow_arrayref(); return $gene_info; } ############################################################################### sub get_gene_info_human_wild { my ($dbh, $gene_name) = @_; my $gene_info = undef; my $string = qq(SELECT human_id, human_id FROM human_gene WHERE human_id LIKE ? LIMIT 0, 100); my $sth_query = $dbh->prepare($string); $sth_query->execute('%' . $gene_name . '%'); while (my @row = $sth_query->fetchrow_array() ) { push @{$gene_info}, \@row; } return $gene_info; } ############################################################################### sub get_gene_info_mouse { my ($dbh, $gene_name) = @_; my $gene_info = undef; my $string = qq(SELECT MGI_id, MGI_name, MGI_descrip, uni_id FROM mouse_gene WHERE MGI_id = ? OR MGI_name = ? OR uni_id = ?); my $sth_query = $dbh->prepare($string); $sth_query->execute('MGI:' . $gene_name, $gene_name, $gene_name); $gene_info = $sth_query->fetchrow_arrayref(); $gene_info->[0] =~ s/^MGI://; return $gene_info; } ############################################################################### sub get_gene_info_mouse_wild { my ($dbh, $gene_name) = @_; my $gene_info = undef; my $string = qq(SELECT MGI_id, MGI_name, MGI_descrip, uni_id FROM mouse_gene WHERE MGI_id LIKE ? OR MGI_name LIKE ? OR uni_id LIKE ? LIMIT 0, 100); my $sth_query = $dbh->prepare($string); $sth_query->execute('%' . $gene_name . '%', '%' . $gene_name . '%', '%' . $gene_name . '%'); while (my @row = $sth_query->fetchrow_array() ) { $row[0] =~ s/^MGI://; push @{$gene_info}, \@row; } return $gene_info; } ############################################################################### sub get_gene_info_rat { my ($dbh, $gene_name) = @_; my $gene_info = undef; my $string = qq(SELECT RGD_id, RGD_name, RGD_descrip, uni_id FROM rat_gene WHERE RGD_id = ? OR RGD_name = ? OR uni_id = ?); my $sth_query = $dbh->prepare($string); $sth_query->execute($gene_name, $gene_name, $gene_name); $gene_info = $sth_query->fetchrow_arrayref(); return $gene_info; } ############################################################################### sub get_gene_info_rat_wild { my ($dbh, $gene_name) = @_; my $gene_info = undef; my $string = qq(SELECT RGD_id, RGD_name, RGD_descrip, uni_id FROM rat_gene WHERE RGD_id LIKE ? OR RGD_name LIKE ? OR uni_id LIKE ? LIMIT 0, 100); my $sth_query = $dbh->prepare($string); $sth_query->execute('%' . $gene_name . '%', '%' . $gene_name . '%', '%' . $gene_name . '%'); while (my @row = $sth_query->fetchrow_array() ) { push @{$gene_info}, \@row; } return $gene_info; } ############################################################################### sub get_gene_info_plasmo { my ($dbh, $gene_name) = @_; my $gene_info = undef; my $string = qq(SELECT plasmo_id, plasmo_id, plasmo_descrip FROM plasmo_gene WHERE plasmo_id = ?); my $sth_query = $dbh->prepare($string); $sth_query->execute($gene_name); $gene_info = $sth_query->fetchrow_arrayref(); return $gene_info; } ############################################################################### sub get_gene_info_plasmo_wild { my ($dbh, $gene_name) = @_; my $gene_info = undef; my $string = qq(SELECT plasmo_id, plasmo_id, plasmo_descrip FROM plasmo_gene WHERE plasmo_id LIKE ? LIMIT 0, 100); my $sth_query = $dbh->prepare($string); $sth_query->execute('%' . $gene_name . '%'); while (my @row = $sth_query->fetchrow_array() ) { push @{$gene_info}, \@row; } return $gene_info; } ############################################################################### sub get_gene_info_dicty { my ($dbh, $gene_name) = @_; my $gene_info = undef; my $string = qq(SELECT dicty_id, dicty_name, dicty_descrip, dicty_syn FROM dicty_gene WHERE dicty_id = ? OR dicty_name = ? OR dicty_syn LIKE ?); my $sth_query = $dbh->prepare($string); $sth_query->execute($gene_name, $gene_name, '%' . $gene_name . '%'); $gene_info = $sth_query->fetchrow_arrayref(); return $gene_info; } ############################################################################### sub get_gene_info_dicty_wild { my ($dbh, $gene_name) = @_; my $gene_info = undef; my $string = qq(SELECT dicty_id, dicty_name, dicty_descrip, dicty_syn FROM dicty_gene WHERE dicty_id LIKE ? OR dicty_name LIKE ? OR dicty_syn LIKE ?); my $sth_query = $dbh->prepare($string); $sth_query->execute('%' . $gene_name . '%', '%' . $gene_name . '%', '%' . $gene_name . '%'); while (my @row = $sth_query->fetchrow_array() ) { push @{$gene_info}, \@row; } return $gene_info; } ############################################################################### sub get_gene_info_eco { my ($dbh, $gene_name) = @_; my $gene_info = undef; my $string = qq(SELECT eco_id, eco_name, eco_descrip, prot_gi FROM eco_gene WHERE eco_id = ? OR eco_name = ? OR uni_id = ? OR gene_id = ? OR ref_gi = ? OR ref_acc = ? OR prot_gi = ? OR prot_acc = ?); my $sth_query = $dbh->prepare($string); $sth_query->execute($gene_name, $gene_name, $gene_name, $gene_name, $gene_name, $gene_name, $gene_name, $gene_name); $gene_info = $sth_query->fetchrow_arrayref(); return $gene_info; } ############################################################################### sub get_gene_info_eco_wild { my ($dbh, $gene_name) = @_; my $gene_info = undef; my $string = qq(SELECT eco_id, eco_name, eco_descrip, prot_gi FROM eco_gene WHERE eco_id LIKE ? OR eco_name LIKE ? OR uni_id LIKE ? OR gene_id LIKE ? OR ref_gi LIKE ? OR ref_acc LIKE ? OR prot_gi LIKE ? OR prot_acc LIKE ?); my $sth_query = $dbh->prepare($string); $sth_query->execute('%' . $gene_name . '%', '%' . $gene_name . '%', '%' . $gene_name . '%', '%' . $gene_name . '%', '%' . $gene_name . '%', '%' . $gene_name . '%', '%' . $gene_name . '%', '%' . $gene_name . '%'); while (my @row = $sth_query->fetchrow_array() ) { #print "[@row]\n"; push @{$gene_info}, \@row; } return $gene_info; } ############################################################################### sub get_synonyms_pombe { my ($dbh, $db_id) = @_; my $string = qq(SELECT synonyms.synonym FROM pombe_synonyms WHERE protein_id = ?); my $sth_query = $dbh->prepare($string); $sth_query->execute($db_id); undef my @synonyms; while (my @row = $sth_query->fetchrow_array() ) { push @synonyms, @row; } return @synonyms; } ############################################################################### sub db_data_check { my ($dbh, $db_id, $primary, $alt_id, $species) = @_; #print "[$db_id] [$primary]\n"; my $species_id = $species_id{$species}; my $tax_id = $species_tax_rev{$species_id}; undef my @data_check; my $kogs_string = qq(SELECT gi_number FROM kog_member WHERE species_id = ? AND (protein_id = ? OR gi_number = ?) ); my $sth_kogs = $dbh->prepare($kogs_string); my $search_id = $db_id; if ($search_id =~ /^ENS/) { $search_id = $primary; } if ($species eq 'S._cerevisiae') { $search_id = $alt_id if defined $alt_id and $alt_id; } elsif ($species eq 'A._thaliana') { $search_id =~ s/\.\d+$//; } elsif ($species eq 'D._melanogaster' or $species eq 'H._sapiens') { my $tmp_id = get_gi_from_id($dbh, $search_id, $tax_id); if (defined $tmp_id and $tmp_id) { $search_id = $tmp_id; } else { my $tmp_id = get_gi_from_id($dbh, $primary, $tax_id); if (defined $tmp_id and $tmp_id) { $search_id = $tmp_id; } else { $tmp_id = get_gi_from_id($dbh, $alt_id, $tax_id); $search_id = $tmp_id if defined $tmp_id and $tmp_id; } } } #print "[$search_id]\n"; $sth_kogs->execute($species_id, $search_id, $search_id); my @kogs = $sth_kogs->fetchrow_array(); #print "KOGS: [$search_id] [$species_id] [@kogs]\n"; if (@kogs) { push @data_check, 'Y'; $gi_query = $kogs[0]; } else { push @data_check, 'N'; } my $inparanoid_string = qq(SELECT * FROM inparanoid_member WHERE uniprot_id = ?); $search_id = $db_id; if ($species eq 'C._elegans') { $search_id = $alt_id; } elsif ($species eq 'D._melanogaster') { $inparanoid_string = qq(SELECT * FROM inparanoid_member WHERE uniprot_id LIKE ?); $search_id = $search_id . '-%'; } elsif ($species eq 'A._thaliana') { $search_id = $primary; $search_id =~ s/\.\d+$//; } elsif ($species eq 'H._sapiens') { $search_id = $ens_query; } elsif ($species eq 'E._coli') { my $tmp_id = get_eco_ref_acc($dbh, $db_id); $search_id = $tmp_id, $search_id =~ s/\.\d+$// if defined $tmp_id and $tmp_id; } my $sth_inparanoid = $dbh->prepare($inparanoid_string); $sth_inparanoid->execute($search_id); my @inpara_keys_excl = qw(ensAM ensCE ensDM ensTN modCB modDP); INP: while (my @inpara = $sth_inparanoid->fetchrow_array() ) { foreach my $excl (@inpara_keys_excl) { if ($inpara[3] =~ /$excl/) { next INP; } } #print "INP: [$search_id] [@inpara]\n"; if (@inpara) { push @data_check, 'Y'; } else { push @data_check, 'N'; } last INP; } #print "INP: [$search_id]\n"; $data_check[1] = 'N' if scalar @data_check == 1; my $homologene_string = qq(SELECT HID FROM homologene WHERE tax_id = ? AND gi_number = ?); my $sth_homologene = $dbh->prepare($homologene_string); $sth_homologene->execute($tax_id, $gi_query); my $homolo = $sth_homologene->fetchrow_arrayref(); #print "HOM [$gi_query]\n"; if ($homolo and defined $homolo) { push @data_check, 'Y'; } else { my $homologene_string = qq(SELECT HID FROM homologene WHERE tax_id = ? AND (gene_symbol = ? OR protein_accession = ?) ); my $sth_homologene = $dbh->prepare($homologene_string); my $search_id = $db_id; if ($species eq 'S._cerevisiae') { $search_id = $alt_id; } elsif ($species eq 'A._thaliana') { $search_id =~ s/\.\d+$//; } #print "HOM [$search_id]\n"; $sth_homologene->execute($tax_id, $search_id, $search_id); my $homolo = $sth_homologene->fetchrow_arrayref(); if ($homolo and defined $homolo) { push @data_check, 'Y'; } else { my $homologene_string = qq(SELECT HID FROM homologene WHERE tax_id = ? AND (gene_symbol = ? OR protein_accession = ?) ); my $sth_homologene = $dbh->prepare($homologene_string); if ($species eq 'A._thaliana') { $primary =~ s/\.\d+$//; } #print "HOM [$primary] [$tax_id]\n"; $sth_homologene->execute($tax_id, $primary, $primary); my $homolo = $sth_homologene->fetchrow_arrayref(); if ($homolo and defined $homolo) { push @data_check, 'Y'; } else { push @data_check, 'N'; } } } my $orthomcl_string = qq(SELECT ome.cluster_id FROM orthomcl_member ome, orthomcl_lookup olo WHERE ome.ortho_id = olo.ortho_id AND ome.org_tlc = ? AND olo.db_id1 = ?); my $search_id = $db_id; if ($species eq 'S._cerevisiae') { $search_id = $alt_id if defined $alt_id and $alt_id; } elsif ($species eq 'E._coli') { my $tmp_id = get_eco_ref_gi($dbh, $db_id); $search_id = $tmp_id if defined $tmp_id and $tmp_id; } elsif ($species eq 'H._sapiens' or $species eq 'M._musculus' or $species eq 'R._norvegicus') { $search_id = $ens_query; $search_id = 'NO_ENS_ID' if not $search_id; } elsif ($species eq 'D._melanogaster') { $orthomcl_string = qq(SELECT ome.cluster_id FROM orthomcl_member ome, orthomcl_lookup olo WHERE ome.ortho_id = olo.ortho_id AND ome.org_tlc = ? AND olo.db_id1 LIKE ?); $search_id = $search_id . '-%'; } elsif ($species eq 'C._elegans') { my $tmp_id = get_worm_wid($dbh, $search_id); if (defined $tmp_id and $tmp_id) { $search_id = $tmp_id; } else { my $tmp_id = get_worm_wid2($dbh, $search_id); $search_id = $tmp_id if defined $tmp_id and $tmp_id; } } my $sth_omcl = $dbh->prepare($orthomcl_string); $sth_omcl->execute($species_3let{$species_id}, $search_id); my @orthomcl = $sth_omcl->fetchrow_array(); #print "OrthoMCL: [$species_3let{$species_id}] [$search_id] [@orthomcl]\n"; if (@orthomcl) { push @data_check, 'Y'; } else { push @data_check, 'N'; } if ($species eq 'S._pombe') { my $vals_string = qq(SELECT * FROM vals_orthologs WHERE pombe_id = ? AND yeast_id != 'none'); my $sth_vals = $dbh->prepare($vals_string); $sth_vals->execute($db_id); my @vals = $sth_vals->fetchrow_array(); if (@vals) { push @data_check, 'Y'; } else { push @data_check, 'N'; } } elsif ($species eq 'S._cerevisiae') { my $vals_string = qq(SELECT * FROM vals_orthologs WHERE pombe_id != 'none' AND yeast_id = ?); my $sth_vals = $dbh->prepare($vals_string); $sth_vals->execute($alt_id); my @vals = $sth_vals->fetchrow_array(); if (@vals) { push @data_check, 'Y'; } else { push @data_check, 'N'; } } return @data_check; } ############################################################################### sub get_kogs_results { my ($dbh, $db_id, $species_id) = @_; my $string = qq(SELECT kog_id FROM kog_member WHERE species_id = ? AND (protein_id = ? OR gi_number = ?) ); my $sth_query = $dbh->prepare($string); $sth_query->execute($species_id, $db_id, $db_id); my @row = $sth_query->fetchrow_array(); #print "[$db_id] [@row]\n"; my $string2 = qq(SELECT * FROM kogs WHERE kog_id = ?); my $sth_query2 = $dbh->prepare($string2); $sth_query2->execute($row[0]); my @row2 = $sth_query2->fetchrow_array(); return @row2; } ############################################################################### sub get_prot_results { my ($dbh, $kog_id) = @_; my $string = qq(SELECT * FROM kog_member WHERE kog_id = ?); my $sth_query = $dbh->prepare($string); $sth_query->execute($kog_id); undef my @prot_ids; while (my @row = $sth_query->fetchrow_array() ) { push @prot_ids, \@row; } return @prot_ids; } ############################################################################### sub get_func_results { my ($dbh, $kog_code) = @_; my $string = qq(SELECT * FROM function WHERE process_key = ?); my $sth_query = $dbh->prepare($string); $sth_query->execute($kog_code); my @row = $sth_query->fetchrow_array(); return @row; } ############################################################################### sub draw_kogs_graph { my ($xaxis_ref, $yaxis_ref) = @_; my $my_graph = GD::Graph::bars->new(260, 120); my @data = ($xaxis_ref, $yaxis_ref); my $max = -1; foreach my $y (@{$yaxis_ref}) { $max = $y if $y > $max; } my $y_max_value = $max; my $y_label_skip = 'auto'; my $y_tick_number = 'auto'; if ($max == 1) { $y_max_value = $max + 1; $y_label_skip = 1; $y_tick_number = 2; } elsif ($max == 2) { $y_label_skip = 1; $y_tick_number = 2; } elsif ($max == 3) { $y_label_skip = 1; $y_tick_number = 3; } if ($y_max_value > 6) { $y_max_value = ( (int($y_max_value/5) + 1)*5); } elsif ($y_max_value > 20) { $y_max_value = ( (int($y_max_value/10) + 1)*10); } $my_graph->set(y_min_value => 0, y_max_value => $y_max_value, y_label => 'No. of orthologs', y_label_skip => $y_label_skip, y_tick_number => $y_tick_number, x_labels_vertical => 1, cycle_clrs => 1, dclrs => ['#ccffcc', '#ffffcc', '#ffddcc', '#ffccff', '#ccddff', '#ccccff', '#cceecc'] ) or die $my_graph->error; $my_graph->set_x_axis_font(GD::gdSmallFont); $my_graph->set_y_axis_font(GD::gdSmallFont); my $gd = $my_graph->plot(\@data) or die $my_graph ->error; my $format = $my_graph->export_format; my $rand = int(rand(100000) ); my ($fpath) = $TMPDIR =~ m|([a-zA-Z0-9_\-/\.]+)|; my $id = Website::Utilities::IdGenerator->get_unique_id(); $fpath .= "/$id.$format"; open GRAPH, ">$fpath" or die qq($fpath: $!); binmode GRAPH; print GRAPH $my_graph->plot(\@data)->$format; close GRAPH; return "$id.$format"; } ############################################################################### sub phy_info { my ($species_count) = shift; undef my @values; undef my $phystring; my $phylink = 0; my $pow2 = 1; foreach my $species_id (@kogs_species_id) { if (exists $species_count->{$species_id}) { $phystring = $phystring . $species_1let{$species_id}; $phylink = ($phylink + $pow2); push @values, $species_count->{$species_id}; } else { $phystring = $phystring . '-'; push @values, 0; } $pow2 *= 2; } return ($phystring, $phylink, @values); } ############################################################################### sub get_inparanoid_results { my ($dbh, $db_id, $species) = @_; my $search_id = $db_id; my $string = qq(SELECT cluster_nr, organism_pair FROM inparanoid_member WHERE uniprot_id = ? ORDER BY organism_pair); if ($species eq 'D._melanogaster') { $string = qq(SELECT cluster_nr, organism_pair FROM inparanoid_member WHERE uniprot_id LIKE ? ORDER BY organism_pair); $search_id = $search_id . '-%'; } my $sth_query = $dbh->prepare($string); $sth_query->execute($search_id); undef my @cluster_numbers; while (my @row = $sth_query->fetchrow_array() ) { push @cluster_numbers, \@row; } undef my @query; if ($species eq 'S._pombe') { @query = ('query', '-', 'modSP', '-', '-', $db_id); } elsif ($species eq 'S._cerevisiae') { @query = ('query', '-', 'modSC', '-', '-', uc($db_id) ); } elsif ($species eq 'C._elegans') { @query = ('query', '-', 'modCE', '-', '-', $db_id); } elsif ($species eq 'A._thaliana') { @query = ('query', '-', 'ncbAT', '-', '-', $db_id); } elsif ($species eq 'D._melanogaster') { @query = ('query', '-', 'modDM', '-', '-', $db_id); } elsif ($species eq 'M._musculus') { @query = ('query', '-', 'modMM', '-', '-', $db_id); } elsif ($species eq 'R._norvegicus') { @query = ('query', '-', 'modRR', '-', '-', $db_id); } elsif ($species eq 'P._falciparum') { @query = ('query', '-', 'sanPF', '-', '-', $db_id); } elsif ($species eq 'H._sapiens') { @query = ('query', '-', 'ensHS', '-', '-', $db_id); } elsif ($species eq 'D._discoideum') { @query = ('query', '-', 'modDD', '-', '-', $db_id); } elsif ($species eq 'E._coli') { @query = ('query', '-', 'ncbEC', '-', '-', $db_id); } undef my @inparanoids; push @inparanoids, \@query; foreach my $prot (@cluster_numbers) { my $string = qq(SELECT * FROM inparanoid_member WHERE cluster_nr = ? AND organism_pair = ? AND uniprot_id != ? ORDER BY organism_pair, inparalog_score DESC); if ($species eq 'D._melanogaster') { $string = qq(SELECT * FROM inparanoid_member WHERE cluster_nr = ? AND organism_pair = ? AND uniprot_id NOT LIKE ? ORDER BY organism_pair, inparalog_score DESC); } my $sth_query = $dbh->prepare($string); $sth_query->execute($prot->[0], $prot->[1], $search_id); while (my @row = $sth_query->fetchrow_array() ) { push @inparanoids, \@row; } } #print "[IN INP: [$db_id]\n"; return @inparanoids; } ############################################################################### sub draw_inparanoid_graph { my ($xaxis_ref, $yaxis_ref) = @_; my $my_graph = GD::Graph::bars->new(540, 150); my @data = ($xaxis_ref, $yaxis_ref); my $max = -1; foreach my $y (@{$yaxis_ref}) { $max = $y if $y > $max; } my $y_max_value = $max; my $y_label_skip = 'auto'; my $y_tick_number = 'auto'; if ($max == 1) { $y_max_value = $max + 1; $y_label_skip = 1; $y_tick_number = 2; } elsif ($max == 2) { $y_label_skip = 1; $y_tick_number = 2; } elsif ($max == 3) { $y_label_skip = 1; $y_tick_number = 3; } if ($y_max_value > 6) { $y_max_value = ( (int($y_max_value/5) + 1)*5); } elsif ($y_max_value > 20) { $y_max_value = ( (int($y_max_value/10) + 1)*10); } $my_graph->set(y_min_value => 0, y_max_value => $y_max_value, y_label => 'No. of orthologs', y_label_skip => $y_label_skip, y_tick_number => $y_tick_number, x_labels_vertical => 1, cycle_clrs => 1, dclrs => ["#ffdfdf", "#efdcaa", "#bbebff", "#8ceffd", "#ffdfff", "#ffccff", "#efe7cf", "#eedcc8", "#f0dcd5", "#ffffcc", "#d2dbd5", "#ffddcc", "#efe7cf", "#d1ffb3", "#f0dcd5", "#ccddff", "#ccccff", "#ccffcc", "#eeeea2", "#c9decb"] ) or die $my_graph->error; $my_graph->set_x_axis_font(GD::gdSmallFont); $my_graph->set_y_axis_font(GD::gdSmallFont); my $gd = $my_graph->plot(\@data) or die $my_graph ->error; my $format = $my_graph->export_format; my $rand = int(rand(100000) ); my ($fpath) = $TMPDIR =~ m|([a-zA-Z0-9_\-/\.]+)|; my $id = Website::Utilities::IdGenerator->get_unique_id(); $fpath .= "/$id.$format"; open GRAPH, ">$fpath" or die qq($fpath: $!); binmode GRAPH; print GRAPH $my_graph->plot(\@data)->$format; close GRAPH; return "$id.$format"; } ############################################################################### sub get_homologene_results { my ($dbh, $db_id, $primary, $species) = @_; my $tax_id = $species_tax_rev{$species_id{$species} }; my $HID_id = ''; my $string = qq(SELECT HID FROM homologene WHERE tax_id = ? AND gi_number = ?); my $sth_query = $dbh->prepare($string); $sth_query->execute($tax_id, $gi_query); my $homolo = $sth_query->fetchrow_arrayref(); if ($homolo and defined $homolo) { $HID_id = $homolo->[0]; } else { my $string = qq(SELECT HID FROM homologene WHERE tax_id = ? AND (gene_symbol = ? OR protein_accession = ?) ); my $sth_query = $dbh->prepare($string); if ($species eq 'A._thaliana') { $db_id =~ s/\.\d+$//; } $sth_query->execute($tax_id, $db_id, $db_id); my $homolo = $sth_query->fetchrow_arrayref(); if ($homolo and defined $homolo) { $HID_id = $homolo->[0]; } else { my $string = qq(SELECT HID FROM homologene WHERE tax_id = ? AND (gene_symbol = ? OR protein_accession = ?) ); my $sth_query = $dbh->prepare($string); if ($species eq 'A._thaliana') { $primary =~ s/\.\d+$//; } $sth_query->execute($tax_id, $primary, $primary); my $homolo = $sth_query->fetchrow_arrayref(); if ($homolo and defined $homolo) { $HID_id = $homolo->[0]; } else { $HID_id = ''; } } } if ($HID_id) { my $string = qq(SELECT * FROM homologene WHERE HID = ?); my $sth_query = $dbh->prepare($string); $sth_query->execute($HID_id); undef my @homologenes; while (my @row = $sth_query->fetchrow_array() ) { push @homologenes, \@row; } return @homologenes; } } ############################################################################### sub draw_homologene_graph { my ($xaxis_ref, $yaxis_ref) = @_; my $my_graph = GD::Graph::bars->new(500, 150); my @data = ($xaxis_ref, $yaxis_ref); my $max = -1; foreach my $y (@{$yaxis_ref}) { $max = $y if $y > $max; } my $y_max_value = $max; my $y_label_skip = 'auto'; my $y_tick_number = 'auto'; if ($max == 1) { $y_max_value = $max + 1; $y_label_skip = 1; $y_tick_number = 2; } elsif ($max == 2) { $y_label_skip = 1; $y_tick_number = 2; } elsif ($max == 3) { $y_label_skip = 1; $y_tick_number = 3; } if ($y_max_value > 6) { $y_max_value = ( (int($y_max_value/5) + 1)*5); } elsif ($y_max_value > 20) { $y_max_value = ( (int($y_max_value/10) + 1)*10); } $my_graph->set(y_min_value => 0, y_max_value => $y_max_value, y_label => 'No. of orthologs', y_label_skip => $y_label_skip, y_tick_number => $y_tick_number, x_labels_vertical => 1, cycle_clrs => 1, dclrs => ["#ffccff", "#eedcc8", "#efdcaa", "#efe7cf", "#f0dcd5", "#ffdfff", "#ffddcc", "#ffdfdf", "#ffffcc", "#ccccff", "#ccddff", "#cceeff", "#ffc848", "#ffe920", "#ffdd75", "#ccffcc", "#d1ffb3", "#c9decb"] ) or die $my_graph->error; $my_graph->set_x_axis_font(GD::gdSmallFont); $my_graph->set_y_axis_font(GD::gdSmallFont); my $gd = $my_graph->plot(\@data) or die $my_graph ->error; my $format = $my_graph->export_format; my $rand = int(rand(100000) ); my ($fpath) = $TMPDIR =~ m|([a-zA-Z0-9_\-/\.]+)|; my $id = Website::Utilities::IdGenerator->get_unique_id(); $fpath .= "/$id.$format"; open GRAPH, ">$fpath" or die qq($fpath: $!); binmode GRAPH; print GRAPH $my_graph->plot(\@data)->$format; close GRAPH; return "$id.$format"; } ############################################################################### sub get_orthomcl_cluster { my ($dbh, $db_id, $species_id) = @_; my $string = qq(SELECT ome.cluster_id FROM orthomcl_member ome, orthomcl_lookup olo WHERE ome.ortho_id = olo.ortho_id AND ome.org_tlc = ? AND olo.db_id1 = ?); if ($species_id eq 'D._melanogaster') { $string = qq(SELECT ome.cluster_id FROM orthomcl_member ome, orthomcl_lookup olo WHERE ome.ortho_id = olo.ortho_id AND ome.org_tlc = ? AND olo.db_id1 LIKE ?); $db_id = $db_id . '-%'; } my $sth_query = $dbh->prepare($string); $sth_query->execute($species_3let{$species_id{$species_id} }, $db_id); my $ortho = $sth_query->fetchrow_arrayref(); #print "[$db_id] [$species_id{$species_id}]";# [@{$ortho}]\n"; return $ortho->[0]; } ############################################################################### sub get_orthomcl_results { my ($dbh, $ortho_id) = @_; my $string = qq(SELECT olo.db_id1, ome.org_tlc, olo.ortho_id FROM orthomcl_member ome, orthomcl_lookup olo WHERE ome.ortho_id = olo.ortho_id AND ome.cluster_id = ? ORDER BY ome.org_tlc, olo.db_id1); my $sth_query = $dbh->prepare($string); $sth_query->execute($ortho_id); undef my @orthomcls; while (my @row = $sth_query->fetchrow_array() ) { push @orthomcls, \@row; } return @orthomcls; } ############################################################################### sub draw_orthomcl_graph { my ($xaxis_ref, $yaxis_ref) = @_; my $my_graph = GD::Graph::bars->new(600, 160); my @data = ($xaxis_ref, $yaxis_ref); my $max = -1; foreach my $y (@{$yaxis_ref}) { $max = $y if $y > $max; } my $y_max_value = $max; my $y_label_skip = 'auto'; my $y_tick_number = 'auto'; if ($max == 1) { $y_max_value = $max + 1; $y_label_skip = 1; $y_tick_number = 2; } elsif ($max == 2) { $y_label_skip = 1; $y_tick_number = 2; } elsif ($max == 3) { $y_label_skip = 1; $y_tick_number = 3; } if ($y_max_value > 6) { $y_max_value = ( (int($y_max_value/5) + 1)*5); } elsif ($y_max_value > 20) { $y_max_value = ( (int($y_max_value/10) + 1)*10); } $my_graph->set(y_min_value => 0, y_max_value => $y_max_value, y_label => 'No. of orthologs', y_label_skip => $y_label_skip, y_tick_number => $y_tick_number, x_labels_vertical => 1, cycle_clrs => 1, dclrs => ["#ffdfdf", "#ccd7ff", "#ccffcc", "#ffffcc", "#cce7ff", "#ffccaa", "#d2dbd5", "#ffc7aa", "#ffddcc", "#bbebff", "#eeeea2", "#cceecc", "#8ceffd", "#ffdfff", "#ffccff", "#cceeff", "#efe7cf", "#ffdd75", "#d1ffb3", "#c9decb", "#f0dcd5", "#ccddff", "#ccccff", "#ffd7aa", "#c9decb"] ) or die $my_graph->error; $my_graph->set_x_axis_font(GD::gdSmallFont); $my_graph->set_y_axis_font(GD::gdSmallFont); my $gd = $my_graph->plot(\@data) or die $my_graph ->error; my $format = $my_graph->export_format; my $rand = int(rand(100000) ); my ($fpath) = $TMPDIR =~ m|([a-zA-Z0-9_\-/\.]+)|; my $id = Website::Utilities::IdGenerator->get_unique_id(); $fpath .= "/$id.$format"; open GRAPH, ">$fpath" or die qq($fpath: $!); binmode GRAPH; print GRAPH $my_graph->plot(\@data)->$format; close GRAPH; return "$id.$format"; } ############################################################################### sub get_val_results { my ($dbh, $db_id) = @_; my $string = qq(SELECT * FROM vals_orthologs WHERE pombe_id = ? OR yeast_id = ?); my $sth_query = $dbh->prepare($string); $sth_query->execute($db_id, $db_id); undef my @vals; while (my @row = $sth_query->fetchrow_array() ) { push @vals, \@row; } return @vals; } ############################################################################### sub search_go_with_ids { my ($dbh, $search_go, $uni_id, $species_id, $local_search_gos) = @_; my $go_flag = 0; GO_SPE: foreach my $go_spe (@go_search_species) { if ($species_id eq $go_spe) { $go_flag = 1; last GO_SPE; } } if ($go_flag) { if ($species_id == 10) { $search_go =~ s/(At.+?)\.\d+$/$1/i; } push @{$local_search_gos}, lc $search_go if $search_go and defined $search_go; my $search_go2 = ''; if ($species_id == 20) { $search_go2 = get_worm_gid($dbh, $search_go); push @{$local_search_gos}, lc $search_go2 if $search_go2 and defined $search_go2; } push @{$local_search_gos}, lc $uni_id if $uni_id and defined $uni_id; #print "[$search_go] [$search_go2] [$uni_id] [@search_gos]\n"; my $search_flag = 0; foreach my $sid (@search_gos) { next unless $sid; if (lc $search_go eq $sid) { $search_flag = 1; last; } if (lc $search_go2 eq $sid) { $search_flag = 1; last; } if (lc $uni_id eq $sid) { $search_flag = 1; last; } } if ($search_flag == 0) { my $go_ids = undef; if ($species_id != 40) { $go_ids = get_go_results($dbh, $species_tax_rev{$species_id}, $search_go); push @search_gos, lc $search_go; } if (not defined $go_ids and $uni_id) { $go_ids = get_go_results_uni($dbh, $species_tax_rev{$species_id}, $uni_id); push @search_gos, lc $uni_id; } if (defined $go_ids) { save_go_info($go_ids, $species_id); } if ($species_id == 20) { my $go_ids2 = undef; $go_ids2 = get_go_results($dbh, $species_tax_rev{$species_id}, $search_go2); push @search_gos, lc $search_go2; if (defined $go_ids2) { save_go_info($go_ids2, $species_id); } } } } return $local_search_gos; } ############################################################################### sub get_go_results { # TODO: if want 'NOT' terms, comment out line != 'NOT' in queries # in this sub-routine and also in get_go_results_uni. # The rest of the code can deal with 'NOT' terms now. my ($dbh, $tax_id, $search_go) = @_; my $sth_query = undef; print ' ' x 2048; if ($tax_id == 3702) { my $string = qq(SELECT DISTINCT go_id, qualifier, evidence FROM go_mappings3 WHERE taxon = ? AND database_name != 'UniProt' AND qualifier != 'NOT' AND (database_id = ? OR database_symbol = ? OR db_synonym LIKE ?) ); $sth_query = $dbh->prepare($string); $sth_query->execute($tax_id, $search_go, $search_go, '%' . $search_go . '%'); } else { my $string = qq(SELECT DISTINCT go_id, qualifier, evidence FROM go_mappings3 WHERE taxon = ? AND database_name != 'UniProt' AND qualifier != 'NOT' AND (database_id = ? OR database_symbol = ?) ); $sth_query = $dbh->prepare($string); $sth_query->execute($tax_id, $search_go, $search_go); } print ' ' x 2048; undef my @go_ids; while (my @row = $sth_query->fetchrow_array() ) { push @go_ids, [ $row[0], $row[1], $row[2] ]; } #@go_ids = # sort { lc $a cmp lc $b } # keys %{ { map { $_->[0], 1 } @go_ids} }; my $go_ids = undef; foreach my $gid (@go_ids) { push @{$go_ids}, [ $gid->[0], $search_go, $gid->[1], $gid->[2] ]; } return $go_ids; } ############################################################################### sub get_go_results_uni { my ($dbh, $tax_id, $search_go) = @_; my $string = qq(SELECT DISTINCT go_id, qualifier, evidence FROM go_mappings3 WHERE taxon = ? AND database_name = 'UniProt' AND qualifier != 'NOT' AND (database_id = ? OR database_symbol = ?) ); my $sth_query = $dbh->prepare($string); print ' ' x 2048; $sth_query->execute($tax_id, $search_go, $search_go); print ' ' x 2048; undef my @go_ids; while (my @row = $sth_query->fetchrow_array() ) { push @go_ids, [ $row[0], $row[1], $row[2] ]; } #@go_ids = # sort { lc $a cmp lc $b } # keys %{ { map { $_, 1 } @go_ids} }; my $go_ids = undef; foreach my $gid (@go_ids) { push @{$go_ids}, [ $gid->[0], $search_go, $gid->[1], $gid->[2] ]; } return $go_ids; } ############################################################################### sub save_go_info { my ($go_ids, $species_id) = @_; my $go_links = ''; foreach my $arr (@{$go_ids}) { my $go_id = $arr->[0]; my $prot_id = $arr->[1]; my $qual = $arr->[2]; my $evid = $arr->[3]; push @{$all_go_ids->{$go_id}{$evid}{$species_3let{$species_id} } }, [$prot_id, $qual]; } } ############################################################################### sub print_go_table { my ($dbh, $orth_title, $local_search_gos) = @_; undef my @go_order; foreach my $go_id (sort keys %{$all_go_ids}) { my $go_type = get_go_type($dbh, $go_id); push @go_order, [$go_id, $go_type]; @go_order = sort { $a->[1] cmp $b->[1] or $a->[0] <=> $b->[0] } @go_order; } undef my @go_rows; my $count = 0; GID: foreach my $go_term (@go_order) { my $go_id = $go_term->[0]; my $go_type = $go_term->[1]; my $go_string = ''; ($count, $go_string) = get_go_string($count, $go_id, $local_search_gos); my $go_desc = get_go_desc($dbh, $go_id); my $go_colour = $go_aspect_colour{$go_type}; #my $href = "http://www.godatabase.org/cgi-bin/amigo/go.cgi?query=$go_id"; my $href = "http://www.godatabase.org/cgi-bin/amigo/go.cgi?view=details&search_constraint=terms&depth=0&query=$go_id"; my $title = 'AmiGO'; my $aspect_href = "http://www.geneontology.org/GO.doc.shtml#$go_aspect_href{$go_type}"; my $aspect_title = $go_aspect_title{$go_type}; $go_desc =~ s|(.{30,50} )|$1", table({-class => 'violet3', -cellpadding => '2' -width => '80%'}, Tr(\@go_table) ), "
"; } else { print "None found."; } print ' ' x 2048; } ############################################################################### sub get_go_string { my ($count, $go_id, $local_search_gos) = @_; my $uni_href = "http://us.expasy.org/cgi-bin/niceprot.pl?"; my $uni_title = 'UniProt'; my $go_string = ''; EVID: foreach my $evid (sort keys %{$all_go_ids->{$go_id} }) { my $evid_string = ''; ORG: foreach my $org (sort keys %{$all_go_ids->{$go_id}{$evid} }) { my $org_string = ''; MID: foreach my $mid (sort @{$all_go_ids->{$go_id}{$evid}{$org} }) { #print "MID: [$mid->[0]]\n"; LID: foreach my $lid (sort @{$local_search_gos}) { #print "LID: [$lid]\n"; if (lc $mid->[0] eq $lid) { $count++; my $href = ''; if ($mid->[0] =~ /^([OPQ][\d][A-Z\d]{3}\d)/i) { $href = a({-href => $uni_href . $mid->[0], -style => $gStyle, -target => $gBlank, -title => $uni_title}, $mid->[0]); } else { $href = a({-href => $species_hrefs{$org} . $mid->[0], -style => $gStyle, -target => $gBlank, -title => $species_href_titles{$org}}, $mid->[0]); } $org_string .= $href; if ($mid->[1] eq 'NOT') { $org_string .= ' [NOT]'; } $org_string .= '", h4("GO terms: "), "
"; print ' ' x 2048; if ($count) { print "", table({-class => 'violet3', -cellpadding => '2', -width => '80%'}, Tr(\@go_table) ), "
"; } else { print "None found."; } print ' ' x 2048; } ############################################################################### sub get_final_go_string { my ($count, $go_id) = @_; my $uni_href = "http://us.expasy.org/cgi-bin/niceprot.pl?"; my $uni_title = 'UniProt'; my $go_string = ''; EVID: foreach my $evid (sort keys %{$all_go_ids->{$go_id} }) { my $evid_string = ''; ORG: foreach my $org (sort keys %{$all_go_ids->{$go_id}{$evid} }) { my $org_string = ''; MID: foreach my $mid (sort @{$all_go_ids->{$go_id}{$evid}{$org} }) { #print "MID: [$mid->[0]]\n"; $count++; my $href = ''; if ($mid->[0] =~ /^([OPQ][\d][A-Z\d]{3}\d)/i) { $href = a({-href => $uni_href . $mid->[0], -style => $gStyle, -target => $gBlank, -title => $uni_title}, $mid->[0]); } else { $href = a({-href => $species_hrefs{$org} . $mid->[0], -style => $gStyle, -target => $gBlank, -title => $species_href_titles{$org}}, $mid->[0]); } $org_string .= $href; if ($mid->[1] eq 'NOT') { $org_string .= ' [NOT]'; } $org_string .= '