';
verGetPost(array('id', 'mtg', 'orfSeq', 'tam', 'start', 'end', 'tamInicial'));
$genopar= new Genopar(__FILE__);
if ($id == '')
$genopar->error("Erro.");
$editor = $UserAuth_username;
$tipos = array('n', 'p');
$ntDir = "../Fasta/$mtg/ORFs/n/";
$aaDir = "../Fasta/$mtg/ORFs/p/";
$fileName = $ntDir."ORF".$id.".fas";
$aaFileName = $aaDir."ORF".$id.".fas";
$seq = '';
$col = 60;
if (!$start || !$end){
$query = "SELECT start, end FROM orf WHERE idMontagem='$mtg' AND id='$id'";
$genopar->abreBanco();
$n = $genopar->queryBanco($query);
if ($n != 1) exit;
$row = $genopar->getArray();
$start = $row['start'];
$end = $row['end'];
$genopar->fechaBanco();
}
$file = fopen($fileName, "r");
$tit = fgets($file, 1024);
if (!$orfSeq){
echo "$tit";
echo "
';
echo "";
}else{
echo "Applying changes...";
$query = "SELECT contigId FROM orf WHERE idMontagem='$mtg' AND id='$id'";
$genopar->abreBanco();
$n = $genopar->queryBanco($query);
if ($n != 1) exit;
$row = $genopar->getArray();
$ctgId = $row['contigId'];
$genopar->fechaBanco();
$dif = $tamInicial - $tam;
$ctgFileName = "../Fasta/$mtg/Contigs/n/Contig$ctgId.fas";
$aaCtgFileName = "../Fasta/$mtg/Contigs/p/Contig$ctgId.fas";
/*
* salvar no arquivo a subsequencia $orfSeq (na ordem em que veio da textarea. se for reversa, o script de update vai arrumar)
*/
$outOrfFile = fopen($fileName, 'w');
fprintf($outOrfFile, "%s%s", $tit, $orfSeq);
if ($start < $end){ #fita normal
$newEnd = $end - $dif;
$newStart = $start;
}else{
$newStart = $start - $dif;
$newEnd = $end;
}
system("cd ../bin && perl updateOrfStart.pl $mtg $ctgId $id $newStart $newEnd");
/*
* bin/updateCtgSeq.pl $ctgFileName $fileName $start $end
*/
system("cd ../bin && perl updateCtgSeq.pl $mtg $ctgFileName $fileName $start $end");
/* bin/nt2aa.pl $fileName $aaFileName
* bin/nt2aa.pl $ctgFileName $aaCtgFileName
*/
system("cd ../bin && perl nt2aa.pl $fileName $aaFileName");
system("cd ../bin && perl nt2aa.pl $ctgFileName $aaCtgFileName");
/* atualizar no banco todas as orfs subsequentes
* SELECT * FROM orf WHERE idMontagem='$mtg' AND contigId=$ctgId AND id > $id
*/
$genopar->abreBanco();
$query = "SELECT id, start, end, frame FROM orf WHERE idMontagem='$mtg' AND contigId=$ctgId AND start > $start";
$genopar->queryBanco($query);
$listaOrf = array();
while($res = $genopar->getArray(MYSQL_ASSOC)){
foreach($res as $key => $value)
$listaOrf[$res['id']][$key] = $value;
}
/* PARA CADA ORF
* CALCULAR NOVO FRAME
* UPDATE orf SET start = start - $dif, end = end - $dif, frame = $novoFrame WHERE idMontagem ='$mtg' AND contigId = $ctgId AND id = $currentOrfId
*/
foreach($listaOrf as $orf){
$newOrfStart = $orf['start'] - $dif;
$newOrfEnd = $orf['end'] - $dif;
$newOrfFrame = calculaFrame($newOrfStart, $newOrfEnd);
$query = "
UPDATE orf
SET
start=$newOrfStart,
end = $newOrfEnd,
frame ='$newOrfFrame'
WHERE
idMontagem ='$mtg' AND
contigId = $ctgId AND
id = '".$orf['id']."'
";
$genopar->queryBanco($query);
}
// ATUALIZA RBS
$query = "
UPDATE rbs
SET
start = start - $dif,
stop = stop - $dif,
position = position - $dif,
old_position = old_position - $dif
WHERE
idMontagem='$mtg' AND
start > $start AND
position > 0";
$genopar->queryBanco($query);
$query = "
UPDATE rbs
SET
position = position - $dif
WHERE
idMontagem='$mtg' AND
id='$id' AND
position > 0";
$genopar->queryBanco($query);
// ATUALIZA START CODON
$query = "
UPDATE startCodons
SET
position = position - $dif,
orfStart = orfStart - $dif
WHERE
idMontagem = '$mtg' AND
idOrf like '".sprintf("%04d", $ctgId)."%' AND
position > $start";
$genopar->queryBanco($query);
// ATUALIZA TRNA
$query = "
UPDATE tRNA
SET
begin = begin - $dif,
end = end - $dif
WHERE
idMontagem = '$mtg' AND
contigId = $ctgId AND
begin > $start";
$genopar->queryBanco($query);
echo "[Done]
";
// Inserir informacao de BLAST desatualizado
$query = "
INSERT INTO edicaoORF
VALUES ('$mtg', '$id', '$editor', CURRENT_DATE (), 0, '')";
$genopar->queryBanco($query);
$genopar->fechaBanco();
system("rm tmp/*\.$mtg\.$contig\.*");
echo "
Refresh the ORF Page to see the modifications.
";
}
function calculaFrame($start, $end){
$frame = $start % 3;
if ($start < $end){
if ($frame == 0)
$frame = 3;
return "F".$frame;
}else{
if ($frame == 2)
$frame = 3;
elseif ($frame == 0)
$frame = 2;
return "R".$frame;
}
}
?>