Re^4: Human genome array

Fair enough. Here's my main code so far:

while (<FILE1>)
{
    if ($_ =~ />/) #Header
    {
        if ($chr_num > 0)
        {
            my @str = split(undef,$temp_str);
            push (@genome,@str);
        }
        $chr_num++;
        print $chr_num . "\n";
        $temp_str = "";
    }
    else
    {
        my $temp = chomp($_);
        $temp_str = $temp_str . $temp;        
    }
}
[download]

I think that I have a problem of line endings or input formatting because I have warnings for unitialized values in: my @str = split(undef,$temp_str)

Comment on Re^4: Human genome array Download Code

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Re^5: Human genome array by toolic (Bishop) on Jul 19, 2011 at 17:44 UTC
To get rid of the `Use of uninitialized value in regexp compilation` warning message, I think you want to use: `my @str = split //, $temp_str;` [download] This will split a string into individual characters.	[reply] [d/l] [select]
Re^5: Human genome array by AR (Friar) on Jul 19, 2011 at 19:34 UTC
That's better, but it would be even better if posted code that was self contained. Also, as many will mention, always `use strict;` and `use warnings;` unless you have a specific reason you're not. I know you're using them, but you should show us you're using them. The main problem I'm seeing in your script is that you're pushing a list into an array. Your description implies you want a matrix. In order to do that, you'll have to push an array reference into your @genome array: `push (@genome,\@str);` Perl only stores scalars in arrays and hash values, so, in order to create a multi-level datastructure, you need fill the array with a reference to the array. A minor thing is that you'll probably miss your last chromosome because of how you're parsing the file. After you hit the end of the file, and there isn't a dangling header, you'll still have a lot of data in $temp_str that doesn't make it into @genome. Edit: also, as toolic says, you should change you split line to: `my @str = split //, $temp_str;`	[reply] [d/l] [select]
Re^5: Human genome array by Not_a_Number (Prior) on Jul 19, 2011 at 18:59 UTC
Hi, uvnew! Perhaps you could elucidate why the answers to your previous post (from 8 months ago) Bioinformatic task failed to solve your problem? Meanwhile, I suggest that you consult the documentation for split. hth, dave	[reply]