$oli->id\n");
$toprint = Convert2Fasta($oli->Sequence);
for ($i=0; $i< count($toprint); $i++) {
fwrite($FastaFile, "$toprint[$i]\n");
}
}
fclose($FastaFile);
// Using the fasta file
// Create the blast database
// and place it in the appropriate directory for wwwblast
$cmd_formatdb = FORMATDB_CMD." -i $blastbasename -p F";
echo "
$cmd_formatdb
";
system($cmd_formatdb, $retval1);
if ($retval1 != 0){
echo "Error while formatting the FASTA database into BLAST format";
exit;
}
echo "BLAST has been updated with the latest oligostock.";
// Create an updated fasta
// file of all plasmids
$qry = "SELECT * FROM plasmids";
$result = mysql_query($qry, $connexion);
$blastbasename = BLAST_HOME . "plasmidstock_db";
$FastaFile = fopen($blastbasename, 'w');
while($pl = mysql_fetch_object($result)) {
//print("**$pl->sequence** ");
if ($pl->sequence != "") {
fwrite($FastaFile, ">$pl->id $pl->Name_\n");
$toprint = Convert2Fasta($pl->sequence);
for ($i=0; $i< count($toprint); $i++) {
fwrite($FastaFile, "$toprint[$i]\n");
}
}
}
fclose($FastaFile);
// Using the fasta file
// Create the blast database
// and place it in the appropriate directory for wwwblast
$cmd_formatdb = FORMATDB_CMD." -i $blastbasename -p F";
echo "
$cmd_formatdb
";
system($cmd_formatdb, $retval1);
if ($retval1 != 0){
echo "Error while formatting the FASTA database into BLAST format";
exit;
}
echo "BLAST has been updated with the latest plasmidstock.";
// Create an updated fasta
// file of all pl_features
$blastbasename = BLAST_HOME . "plfeatstock_db";
$FastaFile = fopen($blastbasename, 'w');
$qry = "SELECT * FROM pl_features";
$result = mysql_query($qry, $connexion);
while($pl = mysql_fetch_object($result)) {
//print("**$pl->sequence** ");
fwrite($FastaFile, ">$pl->Description\n");
$toprint = Convert2Fasta($pl->Sequence);
for ($i=0; $i< count($toprint); $i++) {
fwrite($FastaFile, "$toprint[$i]\n");
}
}
$qry = "SELECT * FROM oligos";
$result = mysql_query($qry, $connexion);
while($feat = mysql_fetch_object($result)) {
//print("**$feat->id** ");
fwrite($FastaFile, ">_$feat->id\n");
$toprint = Convert2Fasta($feat->Sequence);
for ($i=0; $i< count($toprint); $i++){
fwrite($FastaFile, $toprint[$i] . "\n");
}
}
fclose($FastaFile);
// Using the fasta file
// Create the blast database
// and place it in the appropriate directory for wwwblast
$cmd_formatdb = FORMATDB_CMD." -i $blastbasename -p F";
echo "
$cmd_formatdb
";
system($cmd_formatdb, $retval1);
if ($retval1 != 0){
echo "Error while formatting the FASTA database into BLAST format";
exit;
}
echo "BLAST has been updated with the latest plfeatstock.";
// Create an updated PlasMapper fasta
// file of all pl_features
$blastbasename = PLASMAPPER_HOME."dataBase/db_vectorFeature/features.fasta.nt";
$FastaFile = fopen($blastbasename, 'w');
$fasta_content = "";
$qry = "SELECT * FROM pl_features";
$result = mysql_query($qry, $connexion);
while($feat = mysql_fetch_object($result)) {
$descr = str_replace(" ","-",substr($feat->Description, 0, strlen($feat->Description)));
// $descr = $feat->Description;
// echo "***$descr*** ";
fwrite($FastaFile, ">$descr" . "[$feat->Category]{" . $descr . "}," . strlen($feat->Sequence) . " bases, " . md5($feat->Sequence) . " checksum.\n");
$fasta_content .= ">$feat->Description\n";
$toprint = Convert2Fasta($feat->Sequence);
for ($i=0; $i< count($toprint); $i++){
fwrite($FastaFile, $toprint[$i] . "\n");
$fasta_content .= $toprint[$i] . "\n";
}
}
$qry = "SELECT * FROM oligos";
$result = mysql_query($qry, $connexion);
while($feat = mysql_fetch_object($result)) {
//print("**$feat->id** ");
fwrite($FastaFile, ">_$feat->id[OTH]{_$feat->id}," . strlen($feat->Sequence) . " bases, " . md5($feat->Sequence) . " checksum.\n");
$fasta_content .= ">_$feat->id\n";
$toprint = Convert2Fasta($feat->Sequence);
for ($i=0; $i< count($toprint); $i++){
fwrite($FastaFile, $toprint[$i] . "\n");
$fasta_content .= $toprint[$i] . "\n";
}
}
fclose($FastaFile);
// Using the fasta file
// Create the blast database
// and place it in the appropriate directory for wwwblast
$cmd_formatdb = FORMATDB_CMD." -i $blastbasename -p F -o T";
echo "
$cmd_formatdb
";
system($cmd_formatdb, $retval1);
if ($retval1 != 0){
echo "Error while formatting the FASTA database into BLAST format";
exit;
}
$html_feat_cnt = <<PlasMap - Help