", table({-width => '100%', -class => 'violet3'}, Tr({-align => 'center'}, td("
", 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]); } my @data_check = do_summary($dbh, $new_id, $species, $go_term, $gene_info); if ($data_check[0] eq 'Y') { do_kogs($dbh, $new_id, $species, $go_term, $gene_info); } if ($data_check[1] eq 'Y') { do_inparanoid($dbh, $new_id, $species, $go_term, $gene_info); } if ($data_check[2] eq 'Y') { do_homologene($dbh, $new_id, $species, $go_term, $gene_info); } if ($data_check[3] eq 'Y') { do_orthomcl($dbh, $new_id, $species, $go_term, $gene_info); } # Top table? if ($data_check[4] eq 'Y') { do_vals($dbh, $new_id, $species, $go_term, $gene_info); } } disconnect_from_DB($dbh); } print_form(); exit 0; } ############################################################################### sub do_summary { my ($dbh, $new_id, $species, $go_term, $gene_info) = @_; #print Dumper $gene_info; my @data_check = db_data_check($dbh, $gene_info->[0], $gene_info->[1], $gene_info->[3], $species); undef my @namerows; my $href = ''; my $title = ''; my $species_id = $species_id{$species}; my $tax_id = $species_tax_rev{$species_id}; my $tax_href = "http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=$tax_id"; push(@namerows, td({-align => 'left', -cellpadding => '2'}, ['Species', a({-href => $tax_href, -style => 'font-family: Verdana; text-decoration: none', -target => '_blank', -title => 'NCBI Taxonomy'}, $species_name{$species_id} . ' (' . $species_3let{$species_id} . ')')]) ); my $sys_id = $gene_info->[0]; my $descrip = $gene_info->[2]; my $uni_id = ''; if ($species eq 'S._pombe') { $sys_id = make_gene_id($sys_id); $href = "http://www.genedb.org/genedb/Search?organism=S.+pombe&name=$sys_id"; $title = 'GeneDB'; $uni_id = get_pombe_uni_id($dbh, $sys_id); } elsif ($species eq 'S._cerevisiae') { $sys_id = make_gene_id($sys_id); $href = "http://db.yeastgenome.org/cgi-bin/locus.pl?locus=$sys_id"; $title = 'SGD'; } elsif ($species eq 'C._elegans') { $href = "http://www.wormbase.org/db/gene/gene?name=$sys_id"; $title = 'WormBase'; $descrip = $gene_info->[4] if not $descrip; $uni_id = get_worm_uni_id($dbh, $sys_id); } elsif ($species eq 'D._melanogaster') { if ($sys_id =~ /^\d+$/) { $href = "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?list_uids=$sys_id"; $title = 'NCBI'; } else { $href = "http://flybase.net/cgi-bin/fbidq.html?$sys_id"; $title = 'FlyBase'; } } elsif ($species eq 'A._thaliana') { my $arab_gi = get_arab_gi($dbh, $sys_id); $href = "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?list_uids=$arab_gi"; $title = 'NCBI'; #$href = "http://www.arabidopsis.org/servlets/TairObject?type=locus&id=$arab_id"; #$title = 'TAIR'; $descrip = ''; } elsif ($species eq 'M._musculus') { $href = "http://www.informatics.jax.org/searches/accession_report.cgi?id=MGI:$sys_id"; $title = 'MGI'; $uni_id = get_mouse_uni_id($dbh, $sys_id); } elsif ($species eq 'R._norvegicus') { $href = "http://rgd.mcw.edu/tools/genes/genes_view.cgi?id=$sys_id"; $title = 'RGD'; $uni_id = get_rat_uni_id($dbh, $sys_id); } elsif ($species eq 'P._falciparum') { $href = "http://www.genedb.org/genedb/Search?organism=malaria&name=$sys_id"; $title = 'GeneDB'; } elsif ($species eq 'H._sapiens') { $sys_id =~ s/^Hs//; my $tmp_id = get_gi_from_id($dbh, $sys_id, $tax_id); $sys_id = $tmp_id if defined $tmp_id and $tmp_id; $href = "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?list_uids=$sys_id"; $title = 'NCBI'; $descrip = ''; } push(@namerows, td({-align => 'left', -cellpadding => '2'}, ['Systematic ID', a({-href => $href, -style => 'font-family: Verdana; text-decoration: none', -target => '_blank', -title => $title}, $sys_id)]) ); push(@namerows, td({-align => 'left'}, ['Primary name', a({-href => $href, -style => 'font-family: Verdana; text-decoration: none', -target => '_blank', -title => $title}, $gene_info->[1])]) ); my $alt_db_id = ''; if ($species eq 'S._cerevisiae') { $alt_db_id = $new_id; } elsif ($species eq 'C._elegans' or $species eq 'D._melanogaster') { $alt_db_id = $gene_info->[3]; } if ($alt_db_id) { push(@namerows, td({-align => 'left'}, ['Alternative ID', a({-href => $href, -style => 'font-family: Verdana; text-decoration: none', -target => '_blank', -title => $title}, $alt_db_id)]) ); } $descrip = '' if not defined $descrip; if ($descrip) { push(@namerows, td({-align => 'left'}, ['Description', $descrip]) ); } $uni_id = get_uniprot_id2($dbh, $sys_id, $tax_id) if not defined $uni_id or not $uni_id; $uni_id = '' if not defined $uni_id; if ($uni_id) { $href = "http://www.expasy.org/cgi-bin/niceprot.pl?$gene_info->[5]"; push(@namerows, td({-align => 'left'}, ['UniProt link', a({-href => $href, -style => 'font-family: Verdana; text-decoration: none', -target => '_blank', -title => 'UniProt'}, $uni_id)]) ); } if ($species eq 'S._pombe') { my @synonyms = get_synonyms($dbh, $new_id); my $synonyms = ''; foreach my $syn (@synonyms) { $synonyms = $synonyms . $syn . ', '; } $synonyms =~ s/, $//; push(@namerows, td({-align => 'left'}, ['Synonyms', $synonyms]) ); my $href3 = "http://www.sanger.ac.uk/perl/SPGE/geexview?group=3&q=$new_id&scale=log2&scale_min=-2&scale_max=2"; my $href2 = "http://www.sanger.ac.uk/perl/SPGE/geexview?group=2&q=$new_id&scale=linear&scale_auto=on"; my $href1 = "http://www.sanger.ac.uk/perl/SPGE/geexview?group=1&q=$new_id&scale=linear&scale_auto=on"; push(@namerows, td({-align => 'left'}, ['Gene expression " .
"" .
"
" .
"" .
"
"
]) );
}
my $kog_href = "http://www.ncbi.nlm.nih.gov/COG/new/";
my $inp_href = "http://inparanoid.cgb.ki.se/";
my $gdb_href = "http://www.sanger.ac.uk/Projects/S_pombe/";
my $hom_href = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=homologene";
my $ort_href = "http://orthomcl.cbil.upenn.edu/";
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 |
", a({-name => 'gene', -style => 'text-decoration: none'}, h4('Gene summary: ') ), "
"; print ' ' x 2048; print "", table({-width => '40%', -cellpadding => '2', -bgcolor => $species_colour{$species_id} }, Tr(\@namerows) ), "
"; print hr({-align => 'left', -size => '2', -width => '80%'}); return @data_check; } ############################################################################### sub do_kogs { my ($dbh, $new_id, $species, $go_term, $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') { 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 { my $tmp_id = get_gi_from_id($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 => 'text-decoration: none'}, 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_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 = $gene_info->[3]; } my @inparanoid_results = get_inparanoid_results($dbh, $search_inp, $species); # Selected organisms for Inparanoid. my @inpara_keys = qw(ensAG ensCF ensDR ensFR ensGG ensHS ensPT modCE modDD modDM modMM modOG modRR modSC modSP ncbAT ncbEC sanPF); # Not in KOGs or Homologene - so exclude. my @inpara_keys_exlc = qw(ensAM ensCE ensDM ensMM ensRN ensTN modCB modDP); undef my @inpara_keys2; foreach my $inkey (@inpara_keys) { push @inpara_keys2, $species_3let{$inparanoid_species{$inkey} }; } undef my @inpara; undef my @prot_ids; undef my %inparanoid_count; undef my $local_search_gos; 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; my $uni_id = ''; foreach my $excl (@inpara_keys_exlc) { if ($prot->[3] =~ /$excl/) { 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 ($prot->[2] eq $inparanoid_species_rev{$species_id{$species} }) { push @prot_ids, $search_id; } my $href = ''; my $title = ''; if ($prot->[2] =~ /^ens/) { $href = "http://dec2004.archive.ensembl.org/$ensembl_species{$species_id}/geneview?peptide=$search_id"; $title = 'Ensembl'; $uni_id = $gene_info->[5]; } elsif ($prot->[2] =~ /^swt/) { $href = "http://us.expasy.org/cgi-bin/niceprot.pl?$search_id"; $title = 'SwissProt'; } elsif ($prot->[2] eq 'sanPF') { $href = "http://www.genedb.org/genedb/Search?organism=malaria&name=$search_id"; $title = 'GeneDB'; } elsif ($prot->[2] eq 'oryza') { $href = "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?list_uids=$search_id"; $title = 'NCBI'; } elsif ($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 = $tmp_id; } if ($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; } $local_search_gos = search_go_with_ids($dbh, $search_go, $uni_id, $species_id, $local_search_gos); #print Dumper $local_search_gos, "", a({-name => 'inparanoid', -style => 'text-decoration: none'}, h4('Inparanoid results: ') ), "
", "Selected databases only", table({-class => 'violet3', -cellpadding => '2'}, Tr(\@inparanoidheadings) ), "
"; undef my @inparanoidheadings2; push(@inparanoidheadings2, td({-align => 'center', -style => 'font-style: italic'}, ['Species', 'Link to cluster', 'Bootstrap', 'Model organism", table({-class => 'violet3', -cellpadding => '2'}, Tr(\@inparanoid) ), "
"; if ($go_final eq 'No' and $go_term eq 'Yes') { print_go_table($dbh, 'Inparanoid', $local_search_gos); } print_back_to_top(); } ############################################################################### sub do_orthomcl { my ($dbh, $new_id, $species, $go_term, $gene_info) = @_; my $search_orth = $new_id; if ($species eq 'S._cerevisiae') { $search_orth = $gene_info->[0]; } elsif ($species eq 'A._thaliana') { $search_orth = $gene_info->[1]; $search_orth =~ s/\.\d+$//; } elsif ($species eq 'C._elegans') { $search_orth = $gene_info->[3]; } my @orthomcl_results = get_orthomcl_results($dbh, $search_orth, $species); # Selected organisms for OrthoMCL. my @orthomcl_keys = qw(Ath Cel Dme Hsa Sce Spo Ecu Aga Dre Fru Gga Mmu Ptr Rno Osa Pfa Eco Ncr Ame Cfa Ddi Kla Cne Yli Dha Ago Cgl); my @orthomcl_keys_exlc = 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->[2] = ucfirst $prot->[2]; my $species_id = $species_3let_rev{$prot->[2]}; #print "SPECIES: [$species_id] [$prot->[2]]\n"; my $search_id = $prot->[0]; my $key_flag = 0; foreach my $key (@orthomcl_keys) { $key_flag = 1 if $key eq $prot->[2]; } next if $key_flag == 0; my $uni_id = ''; foreach my $excl (@orthomcl_keys_exlc) { if ($prot->[2] =~ /$excl/) { next PROT; } } my $pid_flag = 0; PID: foreach my $pid (@oprot_ids) { if ($search_id eq $pid) { $pid_flag = 1; last PID; } } if ($pid_flag == 0) { $orthomcl_count_hash{$prot->[2]}++; } # if ($prot->[2] eq $inparanoid_species_rev{$species_id{$species} }) { # push @oprot_ids, $search_id; # } my $href = ''; my $title = ''; if ($prot->[2] eq 'Aga' or $prot->[2] eq 'Dre' or $prot->[2] eq 'Fru' or $prot->[2] eq 'Gga' or $prot->[2] eq 'Hsa' or $prot->[2] eq 'Mmu' or $prot->[2] eq 'Rno' or $prot->[2] eq 'Tni') { $href = "http://dec2004.archive.ensembl.org/$ensembl_species{$species_id}/geneview?peptide=$search_id"; $title = 'Ensembl'; } elsif ($prot->[2] eq 'Pfa') { $href = "http://www.genedb.org/genedb/Search?organism=malaria&name=$search_id"; $title = 'GeneDB'; } elsif ($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 'Cel' or $prot->[2] 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->[2] 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->[2] eq 'Sce') { $href = "http://db.yeastgenome.org/cgi-bin/locus.pl?locus=$search_id"; $title = 'SGD'; } elsif ($prot->[2] eq 'Ddi') { $href = "http://dictybase.org/db/cgi-bin/gene_page.pl?dictybaseid=$search_id"; $title = 'dictyBase'; } elsif ($prot->[2] eq 'Dme') { $href = "http://flybase.net/cgi-bin/fbidq.html?$search_id"; $title = 'FlyBase'; } elsif ($prot->[2] eq 'Osa') { $href = "http://www.gramene.org/db/protein/protein_search?acc=$search_id"; $title = 'Gramene'; $uni_id = $search_id; } my $tmp_id = ''; if ($prot->[2] eq 'Dme') { ($tmp_id = $search_id) =~ s/\-(\S+)$//; $tmp_id = get_fly_id($dbh, $tmp_id); } elsif ($prot->[2] eq 'Ath') { $tmp_id = get_arab_id($dbh, $search_id); } if ($tmp_id) { $search_id = $tmp_id; } if ($go_term eq 'Yes') { my $search_go = $search_id; if ($prot->[2] eq 'Mmu') { $search_go = 'MGI:' . $search_go; } elsif ($prot->[2] eq 'Rno') { $search_go = 'RGD:' . $search_go; } $local_search_gos = search_go_with_ids($dbh, $search_go, $uni_id, $species_id, $local_search_gos); } if ($prot->[5] ne $search_id) { $search_id = $prot->[5] . '", a({-name => 'orthomcl', -style => 'text-decoration: none'}, h4('OrthoMCL results: ') ), "
", "Selected databases only", table({-class => 'violet3', -cellpadding => '2'}, Tr(\@orthomclheadings) ), "
"; undef my @orthomclheadings2; push(@orthomclheadings2, td({-align => 'center', -style => 'font-style: italic'}, ['Species', 'Model organism", table({-class => 'violet3', -cellpadding => '2'}, Tr(\@orthomcl) ), "
"; if ($go_term eq 'Yes') { print_go_table($dbh, 'OrthoMCL', $local_search_gos); } print_back_to_top(); } ############################################################################### sub do_homologene { my ($dbh, $new_id, $species, $go_term, $gene_info) = @_; my $search_hom = $gene_info->[1]; my @homologene_results = get_homologene_results($dbh, $new_id, $search_hom, $species); undef my @homologene; undef my @hom; my $HID = ''; undef my $local_search_gos; #print "[@homologene_results]\n"; foreach my $prot (@homologene_results) { $HID = $prot->[0]; my $species_id = $species_tax{$prot->[1]}; my $search_id = $prot->[3]; my $gi = $prot->[4]; 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; } $local_search_gos = search_go_with_ids($dbh, $search_go, $uni_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 = $search_id . ';", a({-name => 'homologene', -style => 'text-decoration: none'}, h4('HomoloGene results: ') ), "
"; print ' ' x 2048; print "", table({-class => 'violet3', -cellpadding => '2'}, Tr(\@hom) ), "
"; undef my @hom2; push(@hom2, td({-align => 'center', -style => 'font-style: italic'}, ['Species', 'Gene ID', 'NCBI link', 'UniProt link']) ); push @hom2, @homologene; print ' ' x 2048; print "", table({-class => 'violet3', -cellpadding => '2'}, Tr(\@hom2) ), "
"; if ($go_term eq 'Yes') { print_go_table($dbh, 'Homologene', $local_search_gos); } print_back_to_top(); } ############################################################################### sub do_vals { my ($dbh, $new_id, $species, $go_term, $gene_info) = @_; my @curated_results = get_val_results($dbh, $new_id); undef my @val_rows; undef my @val; push(@val_rows, td({-align => 'center', -style => 'font-style: italic'}, ['S. pombe", a({-name => 'curated', -style => 'text-decoration: none'}, h4('Curated yeast ortholog results: ') ), "
"; print ' ' x 2048; print "", table({-class => 'violet3', -cellpadding => '2'}, Tr(\@val_rows) ), "
"; if ($go_term eq 'Yes') { print_go_table($dbh, 'curated homolog', $local_search_gos); } print_back_to_top(); } ############################################################################### sub print_form { print start_form(); print p("Search for gene by ID or name: ", textfield("gene", "", 30, 100) ); print p("Query species: ", scrolling_list(-name => 'species', -values => ['A._thaliana', 'C._elegans', 'D._melanogaster', 'H._sapiens', 'M._musculus', 'P._falciparum', 'R._norvegicus', 'S._cerevisiae', 'S._pombe'], -labels => {'A._thaliana' => 'A. thaliana', 'C._elegans' => 'C. elegans', 'D._melanogaster' => 'D. melanogaster', 'H._sapiens' => 'H. sapiens', 'M._musculus' => 'M. musculus', 'P._falciparum' => 'P. falciparum', 'R._norvegicus' => 'R. norvegicus', 'S._cerevisiae' => 'S. cerevisiae', 'S._pombe' => 'S. pombe'}, -size => 1, -default => 'S._pombe') ); print p("Include wild-cards: ", radio_group(-name => 'wild', -values => ['Yes', 'No'], -default => 'No') ); print p("Search for GO info: ", radio_group(-name => 'go', -values => ['Yes', 'No'], -default => 'No') ); print p(submit("Find orthologs"), defaults("Reset") ); print ' ' x 2048; print table({-width => '100%', -cellpadding => '2'}, Tr({-align => 'center', -valign => 'top', -class => 'violet3'}, [td(['', 'webmaster@sanger.ac.uk', '']) ]) ); print end_form(); } ############################################################################### sub print_back_to_top { print a({-href => "#gene", -style => 'text-decoration: none'}, 'Back to the top'); print hr({-align => 'left', -size => '2', -width => '80%'}); } ############################################################################### sub get_gene_info { my ($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, $gene_name); } } return ($gene_info); } ############################################################################### sub get_gene_info_pombe { my ($dbh, $gene_name) = @_; my $gene_info = undef; my $string = qq(SELECT * FROM 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 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 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 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 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 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 = ?) ); my $sth_query = $dbh->prepare($string); $sth_query->execute('WP:' .$gene_name, $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 ?) 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() ) { $row[0] =~ s/^WP://; push @{$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, $gene_name) = @_; #print "[$gene_name]\n"; 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 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 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 $gene_info; } ############################################################################### sub get_synonyms { my ($dbh, $db_id) = @_; my $string = qq(SELECT synonym FROM 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) = @_; 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 = $db_id; if ($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; } } } $sth_kogs->execute($species_id, $search_id, $search_id); my @kogs = $sth_kogs->fetchrow_array(); #print "KOGS: [$search_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; $search_id =~ s/\.\d+$//; } my $sth_inparanoid = $dbh->prepare($inparanoid_string); $sth_inparanoid->execute($search_id); my @inpara_keys_exlc = qw(ensAM ensCE ensDM ensMM ensRN ensTN modCB modDD modDP); INP: while (my @inpara = $sth_inparanoid->fetchrow_array() ) { foreach my $excl (@inpara_keys_exlc) { if ($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 = ? OR olo.db_id2 = ?) ); my $sth_omcl = $dbh->prepare($orthomcl_string); my $search_id = $db_id; if ($species eq 'S._cerevisiae') { $search_id = $alt_id if defined $alt_id and $alt_id; } elsif ($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 ? OR olo.db_id2 LIKE ?) ); $search_id = $search_id . '-%'; } $sth_omcl->execute($species_3let{$species_id}, $search_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_label_skip = 1; $y_tick_number = 1; } elsif ($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_hash) = shift; undef my @values; undef my $phystring; my $phylink = 0; my $pow2 = 1; foreach my $species_id (@kogs_species_id) { if (exists $species_count_hash->{$species_id}) { $phystring = $phystring . $species_1let{$species_id}; $phylink = ($phylink + $pow2); push @values, $species_count_hash->{$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); } 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 = $sth_query->fetchrow_array() ) { #print "[@row]\n"; push @inparanoids, \@row; } } #print "[IN INP: [$db_id]\n"; return @inparanoids; } ############################################################################### sub draw_inparanoid_graph { my ($xaxis_ref, $yaxis_ref) = @_; my $my_graph = GD::Graph::bars->new(500,150); my @data = ($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_label_skip = 1; $y_tick_number = 1; } elsif ($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", "#eedcc8", "#ffffcc", "#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_orthomcl_results { 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 = ? OR olo.db_id2 = ?) ); my $sth_query = $dbh->prepare($string); 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 ? OR olo.db_id2 LIKE ?) ); $db_id = $db_id . '-%'; } $sth_query->execute($species_3let{$species_id{$species_id} }, $db_id, $db_id); my $ortho = $sth_query->fetchrow_arrayref(); print "[$db_id] [$species_id{$species_id}] [@{$ortho}]\n"; if ($ortho and defined $ortho) { my $ortho_id = $ortho->[0]; my $string = qq(SELECT olo.db_id1, olo.db_id2, ome.org_tlc FROM orthomcl_member ome, orthomcl_lookup olo WHERE ome.ortho_id = olo.ortho_id AND ome.cluster_id = ?); my $sth_query = $dbh->prepare($string); $sth_query->execute($ortho_id); undef my @orthomcls; while (my @row = $sth_query->fetchrow_array() ) { push @orthomcls, \@row; } #print Dumper @orthomcls; return @orthomcls; } } ############################################################################### sub get_homologene_results { my ($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 = $sth_query->fetchrow_array() ) { push @homologenes, \@row; } #print Dumper @homologenes; return @homologenes; } } ############################################################################### sub get_val_results { my ($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 = $sth_query->fetchrow_array() ) { push @vals, \@row; } return @vals; } ############################################################################### sub search_go_with_ids { # TODO: Don't search Hsa or Dme KOGs IDs as they are not in GO list! my ($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) { $search_go =~ s/\.\d+$//; } 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 $local_search_gos; } ############################################################################### sub get_go_results { my ($dbh, $tax_id, $search_go) = @_; my $sth_query = undef; print ' ' x 2048; if ($tax_id == 3702) { my $string = qq(SELECT go_id FROM go_mappings2 WHERE taxon = ? AND database_name != 'UniProt' 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 go_id FROM go_mappings2 WHERE taxon = ? AND database_name != 'UniProt' 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]; } @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, $search_go]; } return $go_ids; } ############################################################################### sub get_go_results_uni { my ($dbh, $tax_id, $search_go) = @_; my $string = qq(SELECT go_id FROM go_mappings2 WHERE taxon = ? AND database_name = 'UniProt' 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]; } @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, $search_go]; } 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 = $arr->[1]; push @{$all_go_ids->{$go_id}{$species_3let{$species_id} } }, $prot_id; } } ############################################################################### sub print_go_table { my ($dbh, $orth_title, $local_search_gos) = @_; undef my @go_rows; my $count = 0; GID: foreach my $go_id (sort keys %{$all_go_ids}) { my $go_org_string = ''; ($count, $go_org_string) = get_go_string($count, $go_id, $local_search_gos); #print "[$count] [$go_org_string]\n"; my ($go_desc, $go_type) = get_go_desc($dbh, $go_id); my $href = "http://www.godatabase.org/cgi-bin/amigo/go.cgi?query=$go_id"; my $title = 'AmiGO'; push(@go_rows, td({-class => 'violet1', -align => 'center'}, [a({-href => $href, -style => 'font-family: Verdana; text-decoration: none', -target => '_blank', -title => $title}, $go_id), $go_desc, $go_type, $go_org_string]) ); } undef my @go_headings; push(@go_headings, td({-align => 'center', -style => 'font-style: italic'}, ['GO ID', 'GO term', 'GO aspect', 'Associated with']) ); undef my @go_table; push @go_table, @go_headings; push @go_table, @go_rows; print "", table({-class => 'violet3', -cellpadding => '2'}, Tr(\@go_table) ), "
"; } else { print "None found."; } } ############################################################################### sub get_go_string { my ($count, $go_id, $local_search_gos) = @_; my $go_org_string = ''; ORG: foreach my $org (sort keys %{$all_go_ids->{$go_id} }) { my $local_string = ''; MID: foreach my $mid (sort @{$all_go_ids->{$go_id}{$org} }) { #print "[$mid]\n"; LID: foreach my $lid (sort @{$local_search_gos}) { #print "[$lid]\n"; if (lc $mid eq $lid) { $count++; $local_string .= $mid. ', '; last LID; } } } if ($local_string) { my $colour = $species_colour{$species_3let_rev{$org} }; $local_string =~ s/, $//; $local_string =~ s/MGI://g; $local_string =~ s/RGD://g; $local_string = "" . $org . ' (' . $local_string . ')