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What progress have you made since adding use warnings;?

yeah, i tried with use warnings and use strict, here is the program which i tried.

#!/usr/bin/perl 
use strict; 
use warnings; 
open(FH1,"read.txt"); 
open(FH2,"qual.txt"); 
my @arr1=<FH1>; 
my @arr2=<FH2>; 
my $joi1=join(' ',@arr1); 
my $joi2=join(' ',@arr2); 
my @new=split('>',$joi1); 
my @numbers=split('>',$joi2); 
my @new; 
my @seqid; 
foreach(@new){         
my($seq_id,$seq)=split(/\n/,$_);         
push(@alp,split(' ',$seq));         
push(@seqid,$seq_id); } 
my @numbers; 
my @numid; 
foreach(@numbers){         
my ($num_id,$numb)=split(/\n/,$_);         push(@num,split(' ',$numb))
+;     
push(@numid,$num_id) 
} 
my @keep= grep {$_ < 1 || $num[$_]>=10 || $alp[$_-1] ne $alp[$_-0]} 0.
+.$#num; 
print (join(' ',@alp[@keep]),"\n"); 
print (join(' ',@num[@keep]),"\n");
[download]

the result which i got is

Use of uninitialized value in split at sample.pl line 15,<FH2> line 6.
Use of uninitialized value in split at sample.pl line 21,<FH2> line 6.
Use of uninitialized value in string ne at sample.pl line 24, <FH2> li
+ne 6. 
Use of uninitialized value in join or string at sample.pl line 25, <FH
+2> line 6. 
TGACTTTTGCAAAGCTCGTA TGACTTTTGCAAAGCTCGTA TGACTTTTGCAAAGCTCGTA        
+                                            34 45 34 23 32 43 54 45 3
+4 12 23 45 54 65 34 23 54 42 34 45 34 23 32 43 54 45 34 12 23 45 54 6
+5 34 23 54 42 34 45 34 23 32 43 54 45 34 12 23 45 54 65 34 23 54 42
[download]

Is this problem because i am using more than one string from 2 different files? in the above program, why are we not comparing the character repetition at all? In some cases, if the number is less than 10, but doesnt come into repeted continous characters, it should be removed. Please suggest what can be done. I am not very good at perl :-( Thanks

No. It is because you are being silly. Some important lines of code are:

my @new = split ('>', $joi1);
...
my @new;
..
foreach (@new) {
[download]

Which of the two @new variables do you expect will be used by the for loop?

Why didn't you show us the '"my" variable @new masks earlier declaration in same scope at ...' errors you received or the errors about @alp and @num? Have you actually run the code you've shown us?

It helps us a lot to help you if you give use sample code we can actually run and if you show us the result you get and the result you would like from running the code. Oh, and the sample code and results should be short. For example cleaning up your code a little including fixing all stricture warnings and errors:

use warnings;
use strict;

my $seq = <<DATA;
>s1
AGCTTTTCGGGCAAT
>s2
GCTGCCCCCCATCTT
>s3
TCGTAGCTGAAAATC
DATA
my $num = <<DATA;
>s1
23 43 45 65 76 54 3 34 54 65 7 45 56 87 56
>s2
23 43 23 45 65 45 76 78 34 8 12 32 65 23 25
>s3
12 23 34 45 56 54 43 32 65 43 12 34 75 76 45
DATA

open FH1, '<', \$seq;
open FH2, '<', \$num;
my @arr1    = <FH1>;
my @arr2    = <FH2>;
my $joi1    = join (' ', @arr1);
my $joi2    = join (' ', @arr2);
my @new     = grep length, split ('>', $joi1);
my @numbers = grep length, split ('>', $joi2);
my @seqid;
my @alp;

foreach (@new) {
    my ($seq_id, $seq) = split (/\n/, $_);
    push (@alp, grep /[ACGT]/, split ('', $seq));
    push (@seqid, $seq_id);
}

my @num;
my @numid;
foreach (@numbers) {
    my ($num_id, $numb) = split (/\n/, $_);
    push (@num, split (' ', $numb));
    push (
        @numid, $num_id
        );
}
my @keep =
    grep {$_ < 1 || $num[$_] >= 10 || $alp[$_ - 1] ne $alp[$_ - 0]} 0 
+.. $#num;
print (join ('  ', @alp[@keep]), "\n");
print (join (' ', map {sprintf '%2d', $_} @num[@keep]), "\n");
[download]

prints:

A  G  C  T  T  T  C  G  G  C  A  A  T  G  C  T  G  C  C  C  C  C  A  T
+  C  T  T  T  C  G  T  A  G  C  T  G  A  A  A  A  T  C
23 43 45 65 76 54 34 54 65 45 56 87 56 23 43 23 45 65 45 76 78 34 12 3
+2 65 23 25 12 23 34 45 56 54 43 32 65 43 12 34 75 76 45
[download]

---

Perl reduces RSI - it saves typing

Use of uninitialized value in string ne at sample.pl line 24, <FH2> line 6.

This refers to

my @keep= grep {$_ < 1 || $num[$_]>=10 || $alp[$_-1] ne $alp[$_-0]} 0..$#num;

This statement appears to be incorrectly constructed. I believe the first argument should be a regex, not a logical conditional.

Revised: Please ignore. As this points out, I was wrong.

The posting appears to have been updated considerably... and the specification has shifted. Plus ça change :-(

OK. I give up. I really hope this is something useful and not just homework. The program below gives:

  >s1:  A  G  C  T  T  T  T  C  G  G  G  C  A  A  T
       23 43 45 65 76 54  3 34 54 65  7 45 56 87 56
    ->  A  G  C  T  T  T  C  G  G  C  A  A  T -- dropped 6 10
       23 43 45 65 76 54 34 54 65 45 56 87 56
  >s2:  G  C  T  G  C  C  C  C  C  C  A  T  C  T  T
       23 43 23 45 65 45 76 78 34  8 12 32 65 23 25
    ->  G  C  T  G  C  C  C  C  C  A  T  C  T  T -- dropped 9
       23 43 23 45 65 45 76 78 34 12 32 65 23 25
  >s3:  T  C  G  T  A  G  C  T  G  A  A  A  A  T  C
       12 23 34 45 56 54 43 32 65 43 12 34 75 76 45
    ->  T  C  G  T  A  G  C  T  G  A  A  A  A  T  C -- all kept
       12 23 34 45 56 54 43 32 65 43 12 34 75 76 45

This one gives me in 2 different files..

#!/usr/bin/perl
open FILE,"seq.txt";
open OUT1,">seq.out";
open OUT2,">num.out";
$seq = "";$num = "";
while(<FILE>) {
    if($_ =~ /^>/) {
        push(@seq,$seq) if $seq;
        $seq='';
        push(@seq,"\n$_");
    } else {
        $_ =~ s/\s*$//;
        $seq = $seq.$_;
    }
}
push(@seq,$seq);
close(FILE);
open FILE,"num.txt";
while(<FILE>) {
    if($_ =~ /^>/) {
        push(@num,$num) if $num;
        $num='';
        push(@num,"\n$_");
    } else {
        $_ =~ s/\s*$/ /;
        $num = $num."$_";
    }
}
push(@num,$num);
close(FILE);
while($_ = shift @seq) {
    my @marker;
    if( $_ =~ />/ ) {
        $shead = $_;
        $nhead = shift @num;
        $seq = shift @seq;
        $num = shift @num;
        #print $seq,"\n";
        #print $num,"\n";
        @s = split (//,$seq);
        @n = split (/ /,$num);
        $pre = "null";
        $cnt = 1;
        $arrcnt = -1;
        foreach(@s) {
            if($_ eq $pre) {
                $cnt++;
            }
            else {
                if ($cnt >= 3 && $n[$arrcnt] < 10) {
                    push(@marker,$arrcnt);
                }
                $cnt = 1;
            }
            $pre = $_;
            $arrcnt++;
        }
        $exp = 0;
        foreach(@marker) {
            $_ = $_ - $exp;
            splice(@n,$_,1);
            splice(@s,$_,1);
            $exp++;
        }
        $seq = join(" ",@s);
        $num = join(" ",@n);
                print OUT1 $shead;
                print OUT1 $seq,"\n";
                print OUT2 $shead;
                print OUT2 $num,"\n";
    } 
    else {
        print "give proper input file";
        exit;
    }
}
[download]

THANK U ALL FOR THE HELP...Am learning a lot :)

well...thats "myself" on the above program... THANK U ALL FOR THE HELP...Am learning a lot :)