Re^2: match and mismatch

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
[download]

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
[download]

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";        
    }
    }
}
[download]

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 !!!

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Re^3: match and mismatch by bart (Canon) on Nov 17, 2008 at 03:57 UTC
You should only print the output if $str1 and $str2 are both set, and then, clear them so you don't print them again. The next is very close to your code, but kind of works. You only need to format the output as desired (I don't know where the large numbers come from): #!/usr/bin/perl open(FILE,"align.input") or die "can not open file: $!"; while($var=<FILE>){ if($var=~/^sxoght:/){ ($str1,$str2)=(); @ar=split(/\s+/,$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; } if(defined $str1 and defined $str2) { for($i=0;$i<=length($str1);$i++) { if(substr($str1,$i,1) ne substr($str2,$i,1)){ # this is not in the desired format, yet print substr($str1,$i,1); print substr($str2,$i,1); print "$i\n"; } } ($str1,$str2)=(); } } [download] For the format, I propose to store the results in an array, and print "mismatch:" only if the array isn't empty at the end. `my @mismatch; for($i=0;$i<=length($str1);$i++) { if(substr($str1,$i,1) ne substr($str2,$i,1)){ push @mismatch, "$i." . substr($str1,$i,1) . substr($s +tr2,$i,1); } } if(@mismatch) { print "mismatch: @mismatch\n"; }` [download] After that modification, the output I get for this file is `>hit tstart tend #query qstart matches qend score + probability mismatches >gi\|122939163\|ref\|NM_000165.3\| 1595 1630 SNPSTER4_104_308EFAA +XX:1:1:1694:128 1 35 36 -10 1.000000 1 mismatch: 30.GA >gi\|113412254\|ref\|XR_018775.1\| 1578 1613 SNPSTER4_104_308EFAA +XX:1:1:1608:94 1 36 36 0 0.090884 0 mismatch: 3.GT 34.TG` [download] p.s. There's a possible speed improvement if you XOR (`^`) the two strings, you'll get a string of null bytes for where they are the same and non null where they are not: `my $xor = $str1 ^ $str2; while($xor =~ /[^\0]/g) { my $i = pos($xor) - 1; # or: $-[0] push @mismatch, "$i." . substr($str1,$i,1) . substr($str2, +$i,1); }` [download]	[reply] [d/l] [select]
Re^4: match and mismatch by heidi (Sexton) on Nov 17, 2008 at 04:58 UTC
hi bart, thank u sooo much for the help.. now i know where all i went wrong. will try to avoid such mistakes next time. i am learning a lot from perlmonks.org. thanks again :)	[reply]
Re^3: match and mismatch by Anonymous Monk on Feb 10, 2017 at 05:00 UTC
but u did not define here @var and @ar	[reply]