';
verGetPost(array("contig", "start", "end"));
$fcontig="/genome.local/data/annotV1/fasta/Contigs/Contig".$contig;
if ($start > $end) $reverse= 1;
if ( !(is_readable($fcontig)) )
$genopar->error("
Não foi possível ler contig do arquivo:
$fcontig");
$file = fopen($fcontig, 'r');
$line = fgets($file, 4096); #Eliminar primeira linha
$SEQ='';
for ($linha= 1; !feof($file); $linhas++){
$line = fgets($file, 4096);
$SEQ.= trim($line);
}
$seq= substr($SEQ,$start-1,$end-$start+1);
if ($reverse)
{
$size = $start-$end+1;
$array = str_split(substr($SEQ, 0, $size));
$array = array_reverse($array);
$seq = '';
foreach ($array as $nt){
$seq .= complement($nt);
}
}
$seqn="";
$cols = 50;
$rows = 5;
for($i=0;$i
$seqn";
exit();
}
$genopar = new Genopar(__FILE__);
$genopar->abrePagina("Busca de ORFs");
echo '
';
$genopar->abreBanco('annotV1');
$aaArray = montaArrayAA();
echo '';
if ($processa == "Pesquisar tRNA"){
if ($aa)
{
$aa = substr($aa, 0,3);
}
else
{
$genopar->fechaPagina();
}
if ($aa != "All")
$n= $genopar->queryBanco("SELECT * FROM tRNA where type='$aa'");
else
$n= $genopar->queryBanco("SELECT * FROM tRNA");
if ($n <= 0)
{
$genopar->error("tRNA not found.");
}
else
{
echo '';
echo '
| Type |
Contig |
Start |
End |
AntiCodon |
Sequence |
Score |
';
#&start=".($lin['begin'] - 100)."&end=".($lin['end'] + 100)."
while($lin= $genopar->getArray())
{
$start = $lin['begin'];
$end = $lin['end'];
$fcontig="/genome.local/data/annotV1/fasta/Contigs/Contig".$lin['contig'];
$reverse=0;
if ($start > $end) $reverse= 1;
if ( !(is_readable($fcontig)) )
$genopar->error("
Não foi possível ler contig do arquivo: $fcontig");
$file = fopen($fcontig, 'r');
$line = fgets($file, 4096); #Eliminar primeira linha
$SEQ='';
for ($linha= 1; !feof($file); $linhas++){
$line = fgets($file, 4096);
$SEQ.= trim($line);
}
$seq= substr($SEQ,$start-1,$end-$start+1);
if ($reverse)
{
$size = $start-$end+1;
$array = str_split(substr($SEQ, 0, $size));
$array = array_reverse($array);
$seq = '';
foreach ($array as $nt){
$seq .= complement($nt);
}
}
$seqLink = "".substr($seq, 0, 4)."...";
echo "
| ".$lin['type']." |
".$lin['contig']." |
".$lin['begin']." |
".$lin['end']." |
".$lin['anticodon']." |
".$seqLink." |
".$lin['score']." |
";
}
echo "
";
}
}
echo '';
$genopar->fechaPagina();
######### FUNCOES
function montaArrayAA(){
return(array(
"All",
"Asp - Aspartate",
"Glu - Glutamate",
"Ala - Alanine",
"Arg - Arginine",
"Asn - Asparagine",
"Cys - Cysteine",
"Phe - Phenylalanine",
"Gly - Glycine",
"Gln - Glutamine",
"His - Histidine",
"Ile - Isoleucine",
"Leu - Leucine",
"Lys - Lysine",
"Met - Methionine",
"Pro - Proline",
"Ser - Serine",
"Tyr - Tyrosine",
"Thr - Threonine",
"Trp - Tryptophan",
"Val - Valine",
));
}
?>