note
Cristoforo
Hi,
<p>
What does the input file look like? Are any of [https://www.google.com/search?hl=en&as_q=fastq&as_epq=&as_oq=&as_eq=&as_nlo=&as_nhi=&lr=&cr=&as_qdr=all&as_sitesearch=www.perlmonks.org&as_occt=any&safe=images&as_filetype=&as_rights=|these formats] in the form that you have?
<p>
One problem I see is you are altering an array with pop while iterating over the array and this will likely cause problems.
<p>
Your code:
<c>
foreach $value (@num_value)
{
if ($value<$cut_off)
{
pop(@num_value);
+
}else{
last;
}
}
$sub1=substr($dna,-@num_value);
@qscopy=reverse @num_value;
foreach $value (@qscopy)
{
if ($value<$cut_off)
{
pop(@qscopy);
}else{
last;
}
}
</c>
First you iterate over <b>@num_value</b> popping off elements (wrongly I believe) and then you reverse the array into <b>@gscopy</b> and pop again, (wrongly again I believe), if the amount is less than <b>$cut_off</b>.
1206921
1206921