fechaPagina(); exit;
}
$genopar = new Genopar(__FILE__);
$genopar->abrePagina("Realizar novo BLAST");
echo "
";
echo "";
echo "\n"; ob_flush(); flush();
if (!$_POST['newOrg'])
$genopar->error("ERRO");
verGetPost(array('newOrg', 'nome', 'org'));
echo "Baixando arquivo FASTA referente ao organismo $newOrg do NCBI..."; ob_flush();flush();
$localFile = getFile($genopar, $newOrg, "faa");
if (!$localFile)
$genopar->error("Nao foi possivel fazer o download do arquivo FASTA");
echo "[feito]
"; ob_flush(); flush();
echo "Formatando o Banco de Dados para o BLAST..."; ob_flush();flush();
$blastDB = formatDB($localFile);
echo "[feito]
"; ob_flush(); flush();
$genopar->abreBanco('annotV1');
criarTabela($genopar, $nome, $org);
$orfsDir = "fasta/ORFs/p";
$blastp_reports = "blast_report/blastp";
mkdir($blastp_reports."/$nome");
$outDir = "$blastp_reports/$nome";
blastall($nome, $orfsDir, $blastDB, $outDir, $genopar);
$genopar->fechaBanco();
ob_end_flush();
$genopar->fechaPagina();
###############################################
######## FUNCOES ###############
###############################################
# Conecta via FTP ao NCBI e baixa o arquivo "nome.ext"
function getFile($genopar, $nome, $ext){
$ncbi = "ftp.ncbi.nih.gov";
$USER = "anonymous";
$PASS = "nada@lugar.algum";
$con = ftp_connect($ncbi) or $genopar->error("NCBI indisponível.");
ftp_login($con, $USER, $PASS);
ftp_chdir($con, "genbank/genomes/Bacteria/$nome/") or $genopar->error("Nao foi possivel mudar de diretorio.");
$pattern = "/.$ext$/";
foreach(ftp_nlist($con, ".") as $file){
if (preg_match($pattern, $file)){
$rmtFile = $file;
break;
}
}
$file = "tmp/$file";
$handle = fopen($file, "w");
if (!ftp_fget($con, $handle, $rmtFile, FTP_ASCII, 0)){
$file = NULL;
}
fclose($handle);
ftp_close($con);
return $file;
}
function formatDB($file){
$dbName = substr($file, 0, -4);
$formatDB = "formatdb -i $file -p T -n $dbName";
system($formatDB);
return $dbName;
}
function blastall($nome, $orfsDir, $blastDB, $outDir, $genopar){
$tableName = "blastp_".$nome;
$i=0;
$orfs = array();
if (is_dir($orfsDir)){
$validORFs = getValid($genopar);
$total = count($validORFs);
echo "Rodando BLAST e inserindo informações no Banco...";
foreach ($validORFs as $orf){
$oldP = $p;
$p = round((++$i/$total)*100, 2) ;
$orfFile = "ORF$orf";
$output = "$outDir/$orfFile.blast";
$blastall = "blastall -p blastp -i $orfsDir/$orfFile -d $blastDB -o $output -a4 -b5 -v5";
// usleep(90);
if ($p > ($oldP)){
echo "\n";
ob_flush();
flush();
}
system("$blastall");
system("bin/newBlastp.pl $output $tableName");
}
echo "[feito]
";
ob_flush();
flush();
}
}
function invalid($orf, $genopar){
$invalid = TRUE;
$id = substr($orf, 3);
$q = "SELECT validation FROM annot WHERE id='$id'";
$r = $genopar->queryBanco($q);
if ($r > 0){
$lin = $genopar->getArray();
if ($lin[0] < 0)
return $invalid;
return !$invalid;
}
return $invalid;
}
function getValid($genopar){
$orfs = array();
$q = "SELECT id FROM annot where validation>'0'";
$r = $genopar->queryBanco($q);
if ($r > 0){
while ($lin = $genopar->getArray())
$orfs[] = $lin['id'];
return $orfs;
}
return NULL;
}
function criarTabela($genopar, $tableName = '', $org){
if ($tableName == '')
$genopar->error("Falta nome da tabela a ser criada.");
## Insere $tableName na tabela de blastp_feitos
$q = "INSERT INTO blastp_feitos VALUES ('', 'blastp_$tableName')";
$genopar->queryBanco($q);
$q = "INSERT INTO organismos VALUES ('$org', '$tableName')";
$genopar->queryBanco($q);
## Gera tabela $tableName
$q = "CREATE TABLE `annotV1`.`blastp_$tableName` (
`orf_id` varchar(8) NOT NULL default '',
`GI` varchar(15) default NULL,
`GenBank` varchar(15) default NULL,
`score` int(5) default NULL,
`expect` double unsigned default NULL,
`frame` varchar(15) default NULL,
`description` varchar(255) default NULL,
`alignq_start` int(11) default NULL,
`alignq_end` int(11) default NULL,
`aligns_start` int(11) default NULL,
`aligns_end` int(11) default NULL
) ENGINE=MyISAM DEFAULT CHARSET=latin1";
$genopar->queryBanco($q);
}
?>