foreach and preg_match help

[qnc]

In the following file I want to isolate the lines with # and put the d numbers following the # in an array. The info is stored in an array called $datline and will be transferred to $matches as normal.

6 0 0 5 << NO. OF LOCI, RISK LOCUS, SEXLINKED (IF 1) PROGRAM
0 0.000000 0.000000 0 << MUT LOCUS, MUT RATE, HAPLOTYPE FREQUENCIES (IF 1)
1 2 3 4 5 6
1 2
0.999990 0.000010 << GENE FREQUENCIES
1 << NO. OF LIABILITY CLASSES
0.000000 0.900000 0.900000
3 6 # d22s1169
0.166667 0.166667 0.166667 0.166667 0.166667 0.166667 << GENE FREQUENCIES
3 6 # d22s1163
0.166667 0.166667 0.166667 0.166667 0.166667 0.166667 << GENE FREQUENCIES
3 6 # d22s1154
0.166667 0.166667 0.166667 0.166667 0.166667 0.166667 << GENE FREQUENCIES
3 5 # d22s1174
0.200000 0.200000 0.200000 0.200000 0.200000 << GENE FREQUENCIES
3 7 # d22s277
0.142857 0.142857 0.142857 0.142857 0.142857 0.142857 0.142857 << GENE FREQUENCIES
0 0 << SEX DIFFERENCE, INTERFERENCE (IF 1 OR 2)
0.200000 0.200000 0.200000 0.200000 0.200000 0.000000 << RECOMB VALUES
1 0.1 0.45 << REC VARIED, INCREMENT, FINISHING VALUE

I have seen the following code which seems to do what I want but i am having trouble adapting it

<!--
from http://weblogtoolscollection.com/regex/regex.php

example to emulate getting host name from URL
preg_match("/^(http:\/\/)?([^\/]+)/i","http://www.php.net/index.html", $matches);
$host = $matches[2];

get last two segments of host name
preg_match("/[^\.\/]+\.[^\.\/]+$/", $host, $matches);
echo "domain name is: {$matches[0]}\n";

This example will produce:
domain name is: php.net
-->

Here is my code so far

<?php
$markers = Array(); //Empty array to be filled with markers.
foreach ($datlines as $lnum => $datline) 
{
//CAUTION Arrays start at 0, line numbers at 1
// #\S* in orginal brackets does this mean # followed by space?
  if (preg_match("/^(#)?(\n)$", $datline ,$matches)) 
    {
    $markers[] = $matches[0];
    }
 } 


// check info correct
// array profile
echo "markers and matches from dat file<br />";
print_r($matches);
echo "<br />";
print_r($markers);

// array info
$matches_implode = implode(" " , $matches);
$markers_implode = implode(" " , $markers);
echo "
<br /><br />
matches = $matches_implode <br /> 
markers = $markers <br /><br />";

// check if numbers are is correct
$no_markers = count($markers);
echo "<$no_markers = number of markers";
?>

Will be most grateful for any advice

[Kudose]

Something like this?

<?php

$data = " 6 0 0 5 << NO. OF LOCI, RISK LOCUS, SEXLINKED (IF 1) PROGRAM
0 0.000000 0.000000 0 << MUT LOCUS, MUT RATE, HAPLOTYPE FREQUENCIES (IF 1)
1 2 3 4 5 6
1 2
0.999990 0.000010 << GENE FREQUENCIES
1 << NO. OF LIABILITY CLASSES
0.000000 0.900000 0.900000
3 6 # d22s1169
0.166667 0.166667 0.166667 0.166667 0.166667 0.166667 << GENE FREQUENCIES
3 6 # d22s1163
0.166667 0.166667 0.166667 0.166667 0.166667 0.166667 << GENE FREQUENCIES
3 6 # d22s1154
0.166667 0.166667 0.166667 0.166667 0.166667 0.166667 << GENE FREQUENCIES
3 5 # d22s1174
0.200000 0.200000 0.200000 0.200000 0.200000 << GENE FREQUENCIES
3 7 # d22s277
0.142857 0.142857 0.142857 0.142857 0.142857 0.142857 0.142857 << GENE FREQUENCIES
0 0 << SEX DIFFERENCE, INTERFERENCE (IF 1 OR 2)
0.200000 0.200000 0.200000 0.200000 0.200000 0.000000 << RECOMB VALUES
1 0.1 0.45 << REC VARIED, INCREMENT, FINISHING VALUE ";

$regex = "|#[\x20]d[^\n]+|";

preg_match_all($regex, $data, $output);

echo '<pre>';
print_r($output[0]);
echo '<pre>';
?>

[Kudose]

Actually, this is a little better ... it strips the # and whitespace after it and puts only the d##### in the array...

<?php

$data = " 6 0 0 5 << NO. OF LOCI, RISK LOCUS, SEXLINKED (IF 1) PROGRAM
0 0.000000 0.000000 0 << MUT LOCUS, MUT RATE, HAPLOTYPE FREQUENCIES (IF 1)
1 2 3 4 5 6
1 2
0.999990 0.000010 << GENE FREQUENCIES
1 << NO. OF LIABILITY CLASSES
0.000000 0.900000 0.900000
3 6 # d22s1169
0.166667 0.166667 0.166667 0.166667 0.166667 0.166667 << GENE FREQUENCIES
3 6 # d22s1163
0.166667 0.166667 0.166667 0.166667 0.166667 0.166667 << GENE FREQUENCIES
3 6 # d22s1154
0.166667 0.166667 0.166667 0.166667 0.166667 0.166667 << GENE FREQUENCIES
3 5 # d22s1174
0.200000 0.200000 0.200000 0.200000 0.200000 << GENE FREQUENCIES
3 7 # d22s277
0.142857 0.142857 0.142857 0.142857 0.142857 0.142857 0.142857 << GENE FREQUENCIES
0 0 << SEX DIFFERENCE, INTERFERENCE (IF 1 OR 2)
0.200000 0.200000 0.200000 0.200000 0.200000 0.000000 << RECOMB VALUES
1 0.1 0.45 << REC VARIED, INCREMENT, FINISHING VALUE ";

$regex = "|#[\x20]d[^\n]+|";

preg_match_all($regex, $data, $output);
$output = preg_replace("|#[\x20]|", "", $output[0]);
echo '<pre>';
print_r($output);
echo '<pre>';
?>

[qnc]

Thanks for that

i have used

<?php
$datlines_implode = implode(" " , $datlines);
preg_match_all("/# (d([0-9]+)s([0-9]+))/ms",$datlines_implode,$matches);
print_r($matches); 
$matches_implode = implode(" " , $matches);
echo "<br /><br />matches = $matches_implode";
?>

which is almost there however what If it id not starting with d the only thing I can garntee is that the line will start with 3 and have a # in it

What is the

$regex = "|#[\x20]d[^\n]+|";

for that?

[Kudose]

$regex = "|#[^\n]+|";
preg_match_all($regex, $data, $output);
$output = preg_replace("|#[\x20]|", "", $output[0]);

echo '<pre>'; print_r($output); echo '</pre>';

[qnc]

Almost there

but now it gives
Array
(
[0] => d22s1169
0.166667 0.166667 0.166667 0.166667 0.166667 0.166667 << GENE FREQUENCIES
3 6 d22s1163
0.166667 0.166667 0.166667 0.166667 0.166667 0.166667 << GENE FREQUENCIES
3 6 d22s1154
0.166667 0.166667 0.166667 0.166667 0.166667 0.166667 << GENE FREQUENCIES
3 5 d22s1174
0.200000 0.200000 0.200000 0.200000 0.200000 << GENE FREQUENCIES
3 7 d22s277
0.142857 0.142857 0.142857 0.142857 0.142857 0.142857 0.142857 << GENE FREQUENCIES
0 0 << SEX DIFFERENCE, INTERFERENCE (IF 1 OR 2)
0.200000 0.200000 0.200000 0.200000 0.200000 0.000000 << RECOMB VALUES
1 0.1 0.45 << REC VARIED, INCREMENT, FINISHING VALUE
)

when all i want is the name after the # which in this case is d....

[Kudose]

I dunno about that, cause this works using the same regex...

<?php

$data = " 6 0 0 5 << NO. OF LOCI, RISK LOCUS, SEXLINKED (IF 1) PROGRAM
0 0.000000 0.000000 0 << MUT LOCUS, MUT RATE, HAPLOTYPE FREQUENCIES (IF 1)
1 2 3 4 5 6
1 2
0.999990 0.000010 << GENE FREQUENCIES
1 << NO. OF LIABILITY CLASSES
0.000000 0.900000 0.900000
3 6 # d22s1169
0.166667 0.166667 0.166667 0.166667 0.166667 0.166667 << GENE FREQUENCIES
3 6 # d22s1163
0.166667 0.166667 0.166667 0.166667 0.166667 0.166667 << GENE FREQUENCIES
3 6 # d22s1154
0.166667 0.166667 0.166667 0.166667 0.166667 0.166667 << GENE FREQUENCIES
3 5 # d22s1174
0.200000 0.200000 0.200000 0.200000 0.200000 << GENE FREQUENCIES
3 7 # d22s277
0.142857 0.142857 0.142857 0.142857 0.142857 0.142857 0.142857 << GENE FREQUENCIES
0 0 << SEX DIFFERENCE, INTERFERENCE (IF 1 OR 2)
0.200000 0.200000 0.200000 0.200000 0.200000 0.000000 << RECOMB VALUES
1 0.1 0.45 << REC VARIED, INCREMENT, FINISHING VALUE ";

$regex = "|#[^\n]+|";

preg_match_all($regex, $data, $output);
$output = preg_replace("|#[\x20]|", "", $output[0]);
echo '<pre>';
print_r($output);
echo '<pre>';
?>

Array
(
    [0] => d22s1169
    [1] => d22s1163
    [2] => d22s1154
    [3] => d22s1174
    [4] => d22s277
)

Atleast for me ... http://www.lampphosting.com/regex.php

[qnc]

i must have made a coding error some where let me check?

[qnc]

I think it is to do with the way the data is held

to upload the data from the local machine to the array $datlines

if( !isset($_POST['submit'])) { ?>

<!-- The data encoding type, enctype, MUST be specified as below -->
<form enctype="multipart/form-data" action="<?php echo $_SERVER['PHP_SELF']; ?>" method="POST">
    <!-- MAX_FILE_SIZE must precede the file input field -->
    <input type="hidden" name="MAX_FILE_SIZE" value="30000" />
    <!-- Name of input element determines name in $_FILES array -->
    Ped file: <input name="pedfile" type="file" /><br />
    Dat file: <input name="datfile" type="file" /><br />
    Smp file: <input name="smpfile" type="file" /><br />
    <input type="submit" name="submit" value="Upload Files" />
</form>

 <?php }

else {

  $uploaddir = './'; // same folder as this file set permission to 0777
  $pedupload = $uploaddir . basename($_FILES['pedfile']['name']);
  $datupload = $uploaddir . basename($_FILES['datfile']['name']);
  $smpupload = $uploaddir . basename($_FILES['smpfile']['name']);

  echo '<pre>';
  if (move_uploaded_file($_FILES['pedfile']['tmp_name'], $pedupload) &&
      substr($_FILES['pedfile']['name'],-4) == ".ped") {
    echo "Ped file is valid, and was successfully uploaded.\n";
  } else {
    echo "Possible file upload attack!\n";
  }
  if (move_uploaded_file($_FILES['datfile']['tmp_name'], $datupload)&&
      substr($_FILES['datfile']['name'],-4) == ".dat") {
    echo "Dat file is valid, and was successfully uploaded.\n";
  } else {
    echo "Possible file upload attack!\n";
  }
  if (move_uploaded_file($_FILES['smpfile']['tmp_name'], $smpupload)&&
      substr($_FILES['smpfile']['name'],-4) == ".smp") {
    echo "Smp file is valid, and was successfully uploaded.\n";
  } else {
    echo "Possible file upload attack!\n";
  }

  $pedlines = file($pedupload);
  $datlines = file($datupload);
  $smplines = file($smpupload);

therefore I have been suplimeneting your code with

<?php
echo "preg_match_all and preg_replace<br />";
$regex = "|#[^\n]+|"; 
$datlines_implode = implode(" " , $datlines);
preg_match_all($regex, $datlines_implode, $output); 
$output = preg_replace("|#[\x20]|", "", $output[0]); 
echo '<pre>'; 
print_r($output); 
echo '<pre>'; 
?>

i think that the array is not holding the line breaks when it is uploaded and transefered around.

Any suggestions?

[Kudose]

Dunno what to tell you on that. Other than to try to force the upload in binary ... or maybe your lines are delimited by something other than a newline feed.