LBMC » MyLabStocks

<?php

session_start ();

require("headers.php");

require_once("lib/seq.lib.php");

// Create an updated fasta

// file of all oligos

$qry = "SELECT * FROM oligos";

$result = mysql_query($qry, $connexion);

$blastbasename = BLAST_HOME . "oligostock_db";

$FastaFile = fopen($blastbasename, 'w');

while($oli = mysql_fetch_object($result)) {

  fwrite($FastaFile, ">$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 "<pre>$cmd_formatdb</pre>";

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**<br>");

  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 "<pre>$cmd_formatdb</pre>";

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**<br>");

  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**<br>");

  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 "<pre>$cmd_formatdb</pre>";

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***<br>";

  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**<br>");

  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 "<pre>$cmd_formatdb</pre>";

system($cmd_formatdb, $retval1);

if ($retval1 != 0){

   echo "Error while formatting the FASTA database into BLAST format";

   exit;

}

$html_feat_cnt = <<<EOD

<html>

<head>

  <meta HTTP-EQUIV =" Content-Type" CONTENT =" text/html; charset=iso-8859-1">

  <meta NAME =" Description" CONTENT =" Wishart Pharmaceutical Research Group -

   PlasMap">

   <link rel=stylesheet type="text/css" href="/PlasMapper/style/PlasMapper.css" title="default PlasMap styles" />

  <title>PlasMap - Help</title>

</head>

<body bgcolor="#ffffff">

<pre>

$fasta_content

</pre>

</body>

</html>

EOD;

$html_feat_filename = PLASMAPPER_HOME . "html/feature.html";

$fp = fopen($html_feat_filename, 'w');

fwrite($fp, $html_feat_cnt);

fclose($fp);

echo "BLAST has updated PlasMapper with the latest plasmid's features.";

?>

<center>

<iframe src="/blast/blast.html" width="100%" height="90%" border="0"/>

</center>