Perl: Sort hash to match order of array of cutsites

Question

hello I am having trouble with the following code, with a fasta file (text) in the folder called data in the same folder as the program.

this file is as such

gi|199581428|gb|EU710615.1| Flavobacterium columnare FclIS (fclIS) gene, complete cds ATGGTAGAAACTCAATTTAAAAATACGGATATCGGGTTGATTCCTGAGGATTGGGAAGTGAAACAATTAG GAGAAGTTATAACATTAATTAATGGTCGAGCATATTCTCAGAATGAATTATTATTTAATGGAAAATACAG GGTTTTGAGAGTTGGAAATTTCTTTTCAAGTGACAAATGGTATTGGAGTAATTTAGAATTAGCAAGTAAA TTCTATGTAAATAAAGGGGATTTAATGTATGCTTGGTCTGCATCCTTTGGTCCAAAATTTTGGAAAAACG AAAAGACAATTTACCATTATCATATTTGGAAAATCGAATTATCTGAATATTTAGATAAGTTTTATCTTTT TTATGTACTTGAAAAGGATAAAGAGAATATTTTAAATCAATCACAAGGTGGAACAATGTTTCATATAACT AAGGAATCAATGGAAAAAAGAAAAATTCCAATTCCTTCTTTAAAAGAACAACAAGCCATCGCCGAAGTAT TATCTGATACCGATGCTTGGATAGAAAGCCTTGAAAAACTTATTACTAAAAAACGCTTGGTAAAACAAGG AGCAATGCAACAACTTTTAACACCCAAAGAGGATTGGGAGGTAAAGAAGTTGGGAGAAATAGCTGAAGTT AGAGATGGTACTCACCAAACTCCAACTTACGTAGAAAGTGGAATACCATTTTATAGTGTAGAAAGTGTCA CTAAAAACGATTTCAAGAATACAAAATACATTTCAGAACAAGAACATAAAATTCTTACAAAGTCCTTTAG AATTGAAAAAGGCGATATATTAATGACACGAATTGGGTCAATTGGAGATTGTAAATTAATTGATTGGGAT GTCAATGCAAGTTTTTATGTAAGCTTAGCATTATTAAAAGTAAAACCCATATTTTCAGCTAATTATTTAT GTCACTATTCAAAAACAGA AAATTTCAAAAAAGAGATAGATATAAATTCATTACAATCTGCAATTCCTAA AAAAATAAATCTAGGTCCTATTTCTAACGTAAAAATAGAATTTCCGTCACTTGATGAACAACAACGTATC GCAACCATTCTGTCCGATATGGATGCCGAAATAGAACATTTAGAAAAGAAACTCAACAAAGCCAAGCAAC TCAAACAAGGGATAATGCAACAGTTACTTACGGGTAAAATACGCTTAATTGCTGGGGATTAA

I am having trouble sorting the output when the user STDIN is "AluI", I want to sort the hash so that the outputted hash is sorted by having the '/' site in the output sorted from earliest to latest.

my $DIRNAME = 'data';
my %RE =( 'AatII' => 'GACGTC 5', 'AccI' => 'GTMKAC 2', 'AclI' => 'AACGTT 2', 'AcyI' => 'GRCGYC      2', 'AflII' => 'CTTAAG 1', 'AflIII' => 'ACRYGT 1', 'AgeI' => 'ACCGGT 1', 'AhaIII' => 'TTTAAA 3',    'AhdI' => 'GACNNNNNGTC 6', 'AluI' => 'AGCT 2', );
my $input='';
my @enz = keys %RE;

opendir(my $dh, $DIRNAME) || die 'Error opening directory: ' . $DIRNAME;
  # Get the list of files
  my @filenames = readdir($dh);
  my $file_count = @filenames;
  # Filter out files without .fa extension
  @filenames = grep { /\.fa$/ } @filenames;
  # Sort the filenames
  @filenames = sort @filenames;

  foreach my $filename (@filenames) {
my $fh;
my $path = sprintf('%s/%s', $DIRNAME, $filename);
if (!open($fh, $path)) {print 'Failed to open %s; skipping', $path;
  next;
}

my $header = <$fh>;
chomp $header;

if ($header =~ />gi\|(\d+)\|gb\|(\w+)\.(\d+)\|(.+)$/) {
  print '*' x 80;
  print "\n";
  print "filename: $filename";
  print "\n";
  print "gi number: $1";
  print "\n";
  print "accession number: $2";
  print "\n";
  print "version: $3";
  print "\n";
  print "description: $4";
  print "\n";
  while ($input ne 'quit') {
print "RE:";
$input = <STDIN>;
chomp $input;
foreach (@enz) {
    if ($input =~ /$_/) {
        #print "$_\n";
        my $val = $RE{$_};
        my $real = substr($val, 0, -2);
        my $cut = chop $val;
        my $length = length ($real);
        my %ha;
        my @fragaft = ();
        my @fragbef = ();
        my @endar = ();

        while (my @line = <$fh>) {
            my $join = join "", @line;
            foreach ($join) {
                while ($_ =~ /($real)/g) {
                    my $length = length($&);
                    #print "$length\n";
                    my $pos = length($`);
                    #print "$pos\n";
                    my $end = $pos + $length;
                    push @endar, $end;
                    my $endlen = $end - ($length-$cut);
                    #print "$endlen\n";

                    #print "$join\n";
                    my @fragbef = substr ($join, 0, $endlen);
                    my @fragaft = substr ($join, $endlen);

                    @ha{@fragbef} = @fragaft;


                }
                print "\n\n\t\t\tCUT POSITIONS: $_\n" foreach @endar;
                foreach(keys %ha) { print "\n$_ / $ha{$_}\n"; }
            }
        } 

    }


    }
}
}
}

the output is given here: http://i.stack.imgur.com/17LLb.jpg (I do not have enough reputation to post this picture here) In this case I want the ASDASDA / ASDASDSD order to match the order of the "CUTSITE" at the top, or even better. To show it like this: Cutsite : 1 => A/AAAA Cutsite: 3 => AAA/AAAA Cutsite: 7 => AAAAAA/A, but with newlines.

Any help would be appreciated.

Answer 1

Are you looking for foreach ( sort keys %ha ) { ? – tjd

yea something like that – Khuram Bhatti

It's not only something like that , it's exactly implementing your requirement

I want the ASDASDA / ASDASDSD order to match the order of the "CUTSITE" at the top…

---

Now for the

or even better. To show it like this: Cutsite : 1 => A/AAAA Cutsite: 3 => AAA/AAAA Cutsite: 7 => AAAAAA/A, but with newlines.

Change

                    my @fragbef = substr ($join, 0, $endlen);
                    my @fragaft = substr ($join, $endlen);

to

                    push @fragbef, substr($join, 0, $endlen);
                    push @fragaft, substr($join, $endlen);

and

                print "\n\n\t\t\tCUT POSITIONS: $_\n" foreach @endar;
                foreach(keys %ha) { print "\n$_ / $ha{$_}\n"; }

to

                for (0..$#endar)
                { print "Cutsite: $endar[$_] =>\n$fragbef[$_]/$fragaft[$_]\n" }