Parse a fasta file using PHP

Question

I have a fasta file input.fa which looks like this:

>KJH325_Org_name_strain
ANNTTHWQLPMCVREEDFSC
>IJA254.1_Org_name
HITYYPQLKSSCMART
>ASDL658_Org_name_str
TTILPQWYERSAASMNCFGHDKLCC
and so on.

I want to enter these short sequences into a Mysql table using PHP such that the KJH325(i.e., the ID after the first underscore '_') goes into ID column and the rest Org_name or Org_name_strain goes into the orgname column and the short sequence in the next line goes into sequence column. I have tried this:

<?php
$servername = "localhost";
$dbname = "shortseqdb";

// Create connection
$conn = mysqli_connect($servername, $dbname);

// Check connection
if (!$conn) {
    die("Connection failed: " . mysqli_connect_error());
}
echo "Connected successfully\n\n";

$fasta_file = 'input.fa';
$header='';
$id = '';
$org_name = '';

$lines = file($fasta_file) or die("Unable to open file!");

foreach ($lines as $line) {
   $header = strpos($line, '>'); <---- UPDATED
   if ($header!==false) {
      $key = trim(substr($line, 0, $header));
      $value = trim(substr($line, $header+1));
        list($id, $org_name) = explode("_",$key);


            $sql = "INSERT INTO `seqs` (`ID`, `org_name`, `sequence`) VALUES ($id, $org_name, $value)";
    }
}

if (mysqli_query($conn, $sql)) {
    echo "Values inserted successfully in the table seqs\n";
} else {
    echo "Error inserting values: " . mysqli_error($conn);
}
mysqli_close($conn);

?>

It connects successfully but I am getting the following error:

Connected successfully

Notice: Undefined offset: 1 in C:\xampp\htdocs\test.php on line 26

Error inserting values: No database selected

Could anybody help me where is this script wrong? Thanks!

Answer 1

I found out that the problem was in username and password. I looked into the privileges on XAMPP in the same database and it turned out I had to specify the username and password as well.

$servername = "localhost";
$username = "root";
$password = "";
$dbname = "shortseqdb";
// Create connection
$conn = mysqli_connect($servername, $dbname);

// Check connection
if (!$conn) {
    die("Connection failed: " . mysqli_connect_error());
}
echo "Connected successfully\n\n";
// select a db
mysqli_select_db($conn,"shortseqdb") or die("Could not select the specified database");

And used mysqli_db_connect($connect,dbname) to select the specified database. Then it worked perfectly.

Thanks for your comments.