", 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, $gene_info); } # Top table? if ($data_check[3] 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 $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 |
| Curated | " . "$img4 |
", 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, $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 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 modDD 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 $ortholog_count; undef my $species_count; 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"; $title = 'Ensembl'; } elsif ($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, $local_search_gos); } if ($prot->[5] ne $search_id) { $search_id = $prot->[5] . '", a({-name => 'inparanoid', -style => 'text-decoration: none'}, h4('Inparanoid results: ') ), "
", "Selected databases only", table({-class => 'violet3', -cellpadding => '2'}, Tr(\@inparanoidheadings) ), "
"; undef my @inparanoidheadings2; push(@inparanoidheadings2, td({-align => 'center', -style => 'font-style: italic'}, ['Species', 'Link to cluster', 'Bootstrap', 'Model organism", table({-class => 'violet3', -cellpadding => '2'}, Tr(\@inparanoid) ), "
"; if ($go_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, $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 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 = ?) ); 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 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) = @_; 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] [$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; $search_id =~ s/\.\d+$//; } 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 $homolo) { push @data_check, 'Y'; } else { push @data_check, 'N'; } } } if ($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) = 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); } 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_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 = $sth_query->fetchrow_array() ) { push @homologenes, \@row; } return @homologenes; } } ############################################################################### sub get_val_results { my ($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_mappings 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_mappings 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_mappings 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 . ')