i will write the complete problem i am facing. Here is the input file i am using. 
sxoght: #query  hit     score   probability     qstart  qend    qorien
+tation    tstart  tend    matches mismatches      gapOpening      gap
+s
@SNPSTER4_104_308EFAAXX:1:1:1694:128
GGGATAAGAGAGGTGCATGTTGGTATTTAAGGTAGT
1 alignment(s) -- reports limited to 10 alignment(s)

sxoght: SNPSTER4_104_308EFAAXX:1:1:1694:128     gi|122939163|ref|NM_00
+0165.3|   -10     1.000000        1       36      +       1595    163
+0    35      1   00
Score = -10, P(A|R) = 1.000000
Query:          1 GGGATAAGAGAGGTGCATGTTGGTATTTAAGGTAGT 36
                  |||||||||||||||||||||||||||||| |||||
Sbjct:       1595 GGGATAAGAGAGGTGCATGTTGGTATTTAAAGTAGT 1630

@SNPSTER4_104_308EFAAXX:1:1:1608:94
GCAGTTTTAAGTTATTAGTTTTTAAAATCAGTACTT
14 alignment(s) -- reports limited to 10 alignment(s)

sxoght: SNPSTER4_104_308EFAAXX:1:1:1608:94      gi|113412254|ref|XR_01
+8775.1|   0       0.090884        1       36      +       1578    161
+3    36      0   00
Score = 0, P(A|R) = 0.090884
Query:          1 GCAGTTTTAAGTTATTAGTTTTTAAAATCAGTACTT 36
                  ||| |||||||||||||||||||||||||||||| |
Sbjct:       1578 GCATTTTTAAGTTATTAGTTTTTAAAATCAGTACGT 1613

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this is a big file, though the whole file looks like this. What i am trying to do exactly is to grep the header (sxoght) for display in columns and also to display where there is a mismatch in the alignment between query and sbjct. for this input file, the expected results should look like: 
>gi|122939163|ref|NM_000165.3|    1595    1630    SNPSTER4_104_308EFAA
+XX:1:1:1694:128    1    36    36    -10    1    1.000000    35    
mismatch : 1625.GA        
>gi|113412254|ref|XR_018775.1|    1578    1613    SNPSTER4_104_308EFAA
+XX:1:1:1608:94    1    36    36    0    1    0.090884    36    
mismatch : 1581.GT 1612.TG

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the code which i have written is : 
#!/usr/bin/perl
open(FILE,"align.input") or die "can not open file";
while($var=<FILE>){
    $str1=();$str2=();
    if($var=~/^sxoght:/){
        @ar=split(/\s+/,$var);
    print ">$ar[2]\t$ar[8]\t$ar[9]\t$ar[1]\t$ar[5]\t$ar[10]\t$ar[6]\t$
+ar[3]\t$ar[4]\t$ar[11]\n";
    }
    if($var=~/^Query:/){
        $str1=$var;
        $str1=~s/^Query:\s+//g;
        $str1=~s/\d+\s+//g;
        $str1=~s/\s+//g;
    }
    if($var=~/^Sbjct:/){
        $str2=$var;
        $str2=~s/^Sbjct:\s+//g;
        $str2=~s/\d+\s+//g;
        $str2=~s/\s+//g;
    }
    for($i=0;$i<=length($str1);$i++)
    {
    if(substr($str1,$i,1) ne substr($str2,$i,1)){
        print substr($str1,$i,1);
        print substr($str2,$i,1);
        print "$i\n";        
    }
    }
}

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I am not able to use "strict and warning" because using it doesnt allow me to access the scalar variable outside the loop. In my code, i m trying to extract the positions first, so that i will subtract it from the already stored @arr values of beginning and start. I am having problems with the for loop. I know where i am going wrong, but dont know how to correct it. PLEASEEEE HELP !!!

In reply to Re^2: match and mismatch by heidi
in thread match and mismatch by heidi

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