shell_exec not working with dynamic commands - php

Question

<?php
ini_set('max_execution_time', 864000);
$seq = "D:/Ractip/Sequence.txt";
$mir = "D:/Ractip/mirhominid.txt";
$shandle = fopen($seq, 'r');
$sdata = fread($shandle, filesize($seq));
$mhandle = fopen($mir, 'r');
$mdata = fread($mhandle, filesize($mir));
$sexp = explode(">", $sdata);
$mexp = explode(">", $mdata);
$i = 1;
$a = 1;
$count = count($sexp);
while($i < $count)
{
$name = explode("\n", $mexp[$a]);
$name = explode(" ", $name[0]);
$name1 = explode("\n", $sexp[$i]);
$file2 = "D:\Ractip\mir\\"."$name[1]".".txt";
$file1 = "D:\Ractip\sequence\\"."name1[0]".".txt";
if ($i == 1){
mkdir("D:/Ractip/Interactions/"."$name[1]", 0777);
}
$file = "D:/Ractip/Interactions/"."$name[1]"."/"."$name1[0]"."+"."$name[1]".".txt";
$fhandle = fopen($file, 'w');
$query = "ractip "."$file1"." "."$file2";
$exec = shell_exec($query);
print $exec;
fwrite($fhandle, $exec);
fclose($fhandle);
if ($i == $count){
$i = 1;
$a++;
}else{
$i++;
}
}
?>
This is the script. I am basically using a tool to get results of roughly 37.5 million combinations, so as you can understand it isn't something I can do on my own, therefore came along this script, previously I separated all candidates into individual files and so that is the explanation for the $name variables I'm calling them that way.
The problem is the shell_exec command, a preliminary Google search really did not explain why it is behaving this way, but shell_exec refuses to process dynamic commands, instead if I were to make a static command like ractip xy.txt zy.txt it will process that, what I need to do is build the command and then make the shell_exec process it, which it unfortunately isn't doing, it would be really helpful if someone can explain why this command behaves this way and if there is a workaround to this glitch.
I've finally gotten around to understanding what a guy on a forum meant when he said that these are just some things php doesn't do very well.
Oh yes, and I am deploying it through the browser, dunno if that is any help.

Answer 1

On both Windows and Linux, you'll be better off by keeping all slashes like "/".
Also, looks like you forgot a $ in $file1:
$file2 = "D:/Ractip/mir/" . $name[1] . '.txt';
$file1 = "D:/Ractip/sequence/" . $name1[0] . ".txt";
Finally, just in case, for clarity, I'd write
$query = "ractip '$file1' '$file2'";
or
$query = 'ractip ' . $file1 . ' ' . $file2 ;
You don't really need to quote a single string variable, i.e. $string and "$string" are the same thing. I did quote $file1 and $file2 with single quotes /inside/ $query, because, if the names contain spaces, the ractip utility would get confused as to where one filename stops and another starts. Maybe it's not your case here, but anyway...

Answer 2

What I observed in your code is that in the file names you are passing, the slashes are not properly escaped:
$file2 = "D:\\Ractip\\mir\\"."$name[1]".".txt";
$file1 = "D:\\Ractip\\sequence\\"."name1[0]".".txt";
This might be causing the command to search for a wrong file