perl_n00b has asked for the wisdom of the Perl Monks concerning the following question:

Thank you for all your guys' help so far! I just have 2 more questions about my code.
So far I have this... 
use strict;
use warnings;

my $dir = 'c:\seqs';

opendir(DIR,$dir) 
       or die "unable to open directory $dir:$!";
       
foreach my $file ( grep{/\.seq$/ && -f "$dir/$_"}readdir DIR)
   
{
    my $output_path = "$dir/$file.seq";
    my $input_path  = "$dir/$file";

    open (my $in, '<',  $input_path) or 
        die "Unable to open $input_path: $!";

    open (my $out, '>', $output_path) or 
        die "Unable to open $output_path: $!";
        
    while (<$in>) 
    {
        my $locus =~ /LOCUS\s*(\w+)/;
        s/\^\^/>$locus\n^^\n/g;
        print $out $_;

    }

    close ($in);
    close ($out);
    
    unlink ($input_path) 
             or die "unable to unlink $input_path: $!";
    rename ($output_path, $input_path) or
        die "Unable to rename $output_path to $input_path:$!";
}

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If ^^ is not present I need to add it in with a new line character before the sequence.
Something like... 
while (<$in>) { 
if $in =~ /^^/ { s/\^\^/\n^^/g; 
print $out $_; 
else { s/[a]|[c]|[t]|[g]{6}/^^\n }

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How would I correctly write the else?
I was thinking I could just find a series of bases and add the ^^ before it but I don't know how to get the same series of bases in the substitution.
Also I need to capture the locus name and place it before the ^^ like this but for the life of me I can not get it to capture.
    while (<$in>) 
    {
        my $locus =~ /LOCUS\s*(\w+)/;
        s/\^\^/>$locus\n^^\n/g;
        print $out $_;

    }

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within the file the Locus name is formatted like this 
Created: Tuesday, July 12, 2005 4:17 PM
LOCUS       AJ877263                 663 bp    DNA     linear   INV 15
+-APR-2005

[download]

Thanks for any help in advance!

Replies are listed 'Best First'.
Re: Writing to file part deux
by ikegami (Patriarch) on Jul 23, 2009 at 18:25 UTC
    (It's "deux".)

    but I don't know how to get the same series of bases in the substitution. 

    s/([actg]{6})/...$1.../

    [download]

    Also I need to capture the locus name and place it before the ^^

    You should have gotten a warning saying you were matching against an undefined value. 
    my ($locus) = /LOCUS\s*(\w+)/;

    [download]
[reply]
[d/l]
[select]
      I had tried my ($locus) = /LOCUS\s*(\w+)/; But it still doesn't capture it.
      I have just realized this is because the variable is being overwritten since it is searching line by line in the <$in>.
      How do I get around that?
[reply]
[d/l]
        my $locus;
while (...) {
    ...
    ($locus) = /.../;
    ...
}

        [download]
[reply]
[d/l]
Re: Writing to file part duex
by graff (Chancellor) on Jul 24, 2009 at 03:58 UTC
    Have you tried your while loop like this? 
    my $locus;

while (<$in>) {
    if ( /LOCUS\s+(\w+)/ ) {
        $locus = $1;
    }
    elsif ( /\^\^/ ) {
        if ( $locus ) {
            s/\^\^/>$locus\n^^\n/g;
        }
        else {
            warn "Found ^^ without a preceding LOCUS value\n";
        }
    }
    print $out $_;
}

    [download]
    Part of the problem is that you only want to assign to $locus when you have just read that particular sort of line from the file. If you do this sort of assignment on every line: 
            ( $locus ) = ( /LOCUS\s+(\w+)/ );

    [download]
    then $locus will get cleared every time your regex fails to match a given line of input. So see if the match will work first, and if it does, then assign the result to $locus.

    Another part is that you'll want to know (via STDERR) if you get a situation where a locus value should be plugged in but you don't have one yet.

    (I hope I understood the question -- not sure that I did...)

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[d/l]
[select]
      @Graff Bingo!

      Thank you everyone!
[reply]

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