Algorithms
How to read fasta sequences from a file using PHP?
Here is a simple function in PHP to read fasta sequences from a file.
Your multifasta input file is “input.fasta”.
function read_fastas($filename){
$fh = fopen($filename, 'r');
$i= 0 ;
$sequences = array();
while($line = fgets($fh)){
$i++;
if($i%2==1){
$sequence['header'] = $line;
}
else{
$sequence['sequence'] = $line;
array_push($sequences, $sequence);
}
}
return $sequences;
}
The rest of the script would go like this:
<?php
$filename = "input.fasta";
//Define function
function read_fastas($filename){
$fh = fopen($filename, 'r');
if (filesize($x) == 0) { //check if file is empty or not
echo "Input file is empty!";
}
else{
$i= 0 ;
$sequences = array();
while($line = fgets($fh)){
$i++;
if($i%2==1){
$sequence['header'] = $line;
}
else{
$sequence['sequence'] = $line;
array_push($sequences, $sequence);
}
}
return $sequences;
}
}
//Call the function
read_fastas();
//do something with your fasta
?>
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