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detail.html
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detail.html
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<style> .fixedfont { font-size : 14px } </style>
<input type="hidden" name="species" value="<% $information->{species} %>">
<input type="hidden" name="accession" value="<% $information->{accession} %>">
<%init>
my $information;
my $stmt = qq"SELECT species, genome_id FROM gene_info WHERE accession = ?";
my $species_genome_id = $db->MySelect(statement => $stmt, type => 'row', vars => [$accession]);
my $species = $species_genome_id->[0];
my $genome_id = $species_genome_id->[1];
my $mt = "mfe_$species";
$mt = "mfe_virus" if ($mt =~ /virus/);
my $bt = "boot_$species";
$bt = 'boot_virus' if ($bt =~ /virus/);
$information->{species} = $species;
$information->{accession} = $accession;
$information->{slipstart} = $slipstart;
$db->Remove_Duplicates($accession);
my ($detail_stmt, $info);
if (!defined($slipstart) and !$mfeid) {
$detail_stmt = qq"SELECT $mt.*, gene_info.genename FROM $mt,gene_info WHERE gene_info.genome_id = ? AND gene_info.genome_id = $mt.genome_id ORDER BY start, seqlength DESC, mfe_method DESC";
$info = $db->MySelect(statement => $detail_stmt, vars => [$genome_id,], type => 'list_of_hashes') or Callstack(message => $detail_stmt , die => 0);
} elsif (!$slipstart) { ## then mfeid is defined
$detail_stmt = qq"SELECT $mt.*, gene_info.genename FROM $mt,gene_info WHERE gene_info.genome_id = ? AND gene_info.genome_id = $mt.genome_id AND $mt.id = ? ORDER BY seqlength DESC, mfe_method DESC";
$info = $db->MySelect(statement => $detail_stmt, vars => [$genome_id,$mfeid], type => 'list_of_hashes') or Callstack(message => $detail_stmt, die => 0);
} else {
$detail_stmt = qq"SELECT $mt.*, gene_info.genename FROM $mt,gene_info WHERE gene_info.genome_id = ? AND gene_info.genome_id = $mt.genome_id AND $mt.start = ? ORDER BY seqlength DESC, mfe_method DESC";
$info = $db->MySelect(statement => $detail_stmt, vars => [$genome_id,$slipstart], type => 'list_of_hashes') or Callstack(message => $detail_stmt, die => 0);
}
foreach my $entry_count (0 .. $#$info) {
foreach my $info_key (keys %{$info->[$entry_count]}) {
$information->{$info_key} = $info->[$entry_count]->{$info_key};
}
$information->{pk_input} =~ tr/atgcu/ATGCU/;
$information->{parsed} =~ s/\s+//g;
my @in = split(//, $information->{sequence});
my @par = split(//, $information->{parsed});
my @parens = split(//, $information->{parens});
## Added 2016-02 for better PARENS
sub open_close {
my $in = shift;
if ($in eq "(" or $in eq "[" or $in eq "<" or $in eq "{") {
return("open");
} elsif ($in eq ")" or $in eq "]" or $in eq ">" or $in eq "}") {
return("close");
} else {
return("unkown");
}
} # End open_close
if (!$information->{new_parens}) {
my $paren_string = "";
## print "No new parens!\n";
PLOOP: for my $c (0 .. $#par) {
my $old_paren = $parens[$c];
my $stem_num = $par[$c];
if ($stem_num eq ".") {
$paren_string .= ".";
next PLOOP;
}
my $stem_type = open_close($old_paren);
my $stem_mod = $stem_num % 4;
if ($stem_type eq "open") {
if ($stem_mod == 0) {
$paren_string .= '<';
} elsif ($stem_mod == 1) {
$paren_string .= '(';
} elsif ($stem_mod == 2) {
$paren_string .= '{';
} elsif ($stem_mod == 3) {
$paren_string .= '[';
} else {
$paren_string .= '/';
}
} elsif ($stem_type eq "close") {
if ($stem_mod == 0) {
$paren_string .= '>';
} elsif ($stem_mod == 1) {
$paren_string .= ')';
} elsif ($stem_mod == 2) {
$paren_string .= '}';
} elsif ($stem_mod == 3) {
$paren_string .= ']';
} else {
$paren_string .= '|';
}
} else {
$paren_string .= "?";
}
}
$information->{parens} = $paren_string;
} else {
$information->{parens} = $information->{new_parens};
}
my $misc = new SeqMisc(sequence => \@in);
$information->{gc_content} = $misc->{gc_content};
$information->{gc_stems} = $misc->Get_GC(\@in, \@par);
my $delta = $information->{seqlength} - length($information->{parsed});
$information->{parsed} .= '.' x $delta;
$information->{brackets} .= '.' x $delta;
$information->{minus_string} = HTMLMisc::Make_Minus($information->{sequence});
$information->{color_minus} = HTMLMisc::Color_Stems($information->{minus_string}, $information->{parsed}, $config->{graph_stem_colors});
# $information->{minus_stop} = HTMLMisc::Color_Stems($information->{color_minus}, $information->{parsed}, $config->{graph_stem_color});
$information->{numbers} = HTMLMisc::Make_Nums($information->{sequence});
$information->{pk_input_colored} = HTMLMisc::Color_Stems($information->{sequence}, $information->{parsed}, $config->{graph_stem_colors});
$information->{brackets_colored} = HTMLMisc::Color_Stems($information->{parens}, $information->{parsed}, $config->{graph_stem_colors});
$information->{parsed_colored} = HTMLMisc::Color_Stems($information->{parsed}, $information->{parsed}, $config->{graph_stem_colors});
## Check the status of the randomized distribution
my $boot_stmt = qq"SELECT mfe_values, mfe_mean, mfe_sd, mfe_se, zscore FROM $bt WHERE mfe_id = ?";
my $boot_info = $db->MySelect(statement => $boot_stmt, type => 'row', vars=>[$information->{id}],);
my $boot;
if (!defined($boot_info) and $config->{do_boot} == 2) {
## Add it to the webqueue
$db->Set_Queue(id => $information->{genome_id}, queue_table => 'webqueue');
} elsif (!defined($boot_info) and $config->{do_boot} == 1) {
$m->comp('generate_boot.html', information => $information); ## , width => 11, height => 1,
my $data = ">tmp
$information->{sequence}
";
my $inputfile = $db->Sequence_to_Fasta($data);
eval "use Bootlace; 1";
$boot = new Bootlace(config => $config,
genome_id => $information->{genome_id},
nupack_mfe_id => $information->{id},
pknots_mfe_id => $information->{id},
inputfile => $inputfile,
species => $information->{species},
accession => $information->{accession},
start => $information->{start},
seqlength => $information->{seqlength},
iterations => $config->{boot_iterations},
boot_mfe_methods => $config->{boot_mfe_methods},
randomizers => $config->{boot_randomizers},);
use Data::Dumper;
print Dumper $boot_info;
$boot_info = $boot->Go();
$db->Put_Boot($boot_info);
chdir($ENV{PRFDB_HOME});
}
## Theoretically we should now have the randomized distribution set,
## But for weird data this will not be, so after we make the feynman we
## will revisit this...
my $acc_slip = qq"$accession-$information->{slipstart}";
my $feynman_pic = new PRFGraph(config=> $config, mfe_id => $information->{id}, accession => $accession);
$information->{feynman_url} = $feynman_pic->Picture_Filename(type=> 'feynman', url => 'url',);
my $feynman_output_filename = $feynman_pic->Picture_Filename(type => 'feynman',);
my $feynman_dimensions = {};
if (!-r $feynman_output_filename) {
$feynman_dimensions = $feynman_pic->Make_Feynman();
} else {
$feynman_dimensions = $feynman_pic->Get_Feynman_ImageSize($feynman_output_filename);
}
$information->{feynman_height} = $feynman_dimensions->{height};
$information->{feynman_width} = $feynman_dimensions->{width};
## Revisiting the Boot and making the graph for it
print "TESTME: $boot_info\n";
if (defined($boot_info)) {
my $mfe_values = $boot_info->[0];
$mfe_values =~ s/^\s+//g;
my @mfe_values_array = split(/\s+/, $mfe_values);
my $chart = new PRFGraph(config => $config, real_mfe => $information->{mfe},
list_data => \@mfe_values_array, accession => $acc_slip, mfe_id => $information->{id},);
my $ppcc_values = $chart->Get_PPCC();
my $filename = $chart->Picture_Filename(type => 'distribution');
my $pre_charturl = $chart->Picture_Filename(type => 'distribution', url => 'url');
$information->{charturl} = $pre_charturl;
if (!-r $filename) {
$chart = $chart->Make_Distribution();
}
$information->{mfe_mean} = $boot_info->[1];
$information->{mfe_sd} = $boot_info->[2];
$information->{mfe_se} = $boot_info->[3];
$information->{boot_db} = $boot_info->[4];
if ($information->{mfe_sd} == 0) {
$information->{zscore} = 0;
} else {
$information->{mfe} = 0 if (!defined($information->{mfe}));
$information->{mfe_mean} = 0 if (!defined($information->{mfe_mean}));
$information->{mfe_sd} = 1 if (!defined($information->{mfe_sd}));
$information->{zscore} = sprintf("%.2f", ($information->{mfe} - $information->{mfe_mean}) / $information->{mfe_sd});
}
$information->{randmean} = sprintf("%.1f", $information->{mfe_mean});
$information->{randse} = sprintf("%.1f", $information->{mfe_se});
$information->{ppcc} = sprintf("%.4f", $ppcc_values);
} else { ##Boot is not defined!
$information->{chart} = "undef";
$information->{charturl} = qq"$ENV{PRFDB_HOME}/html/no_data.gif";
$information->{mfe_mean} = "undef";
$information->{mfe_sd} = "undef";
$information->{mfe_se} = "undef";
$information->{zscore} = "UNDEF";
$information->{randmean} = "UNDEF";
$information->{randse} = "UNDEF";
$information->{ppcc} = "UNDEF";
}
## Now we should have the randomized distribution picture created.
$m->comp('single_detail.html', information=>$information,);
} ## End foreach structure in the database
my $num_algos = 0;
$num_algos++ if ($config->{do_pknots} == 1);
$num_algos++ if ($config->{do_nupack} == 1);
$num_algos++ if ($config->{do_hotknots} == 1);
my $num_expected_mfes = scalar(@{$config->{seqlength}}) * $num_algos;
my $num_have = $db->MySelect(statement => qq"SELECT count(id) FROM $mt WHERE accession = '$accession' AND start = '$slipstart'", type => 'single');
$db->Put_Webqueue($information->{genome_id}) if ($num_have < $num_expected_mfes);
</%init>
<%args>
$accession => 'SGDID:S000001';
$slipstart => undef;
$mfeid => undef;
</%args>