Compare two variables

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

Hello! I hope my problem is more complicated than the title suggests. I need to compare a series of 100 sequences with the original and the program should give me one number of identities. For example:

Original sequence: ATCGGGACG 
Stream 0:          TCGTCAGCG
Sequence 1:        ATGCGAAAA
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Then the program should print:

The sequence 0 has 2 identities
The sequence 1 has 4 identities
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My code requires a file containing the original sequence (you will note this at the biginning, where it says: "original.FASTA") so I don't know if you can work without it. Thanks already.

#!/usr/bin/perl -w
#Lectura de archivo de secuencias
$secuencia = 'original.FASTA';
#Abrir el archivo
open (SECUENCIA, $secuencia);
#Leer la secuencia
@secuencia = <SECUENCIA>;
close SECUENCIA;
#Eliminar la línea de título.
$secuencia[0]="";
#print "Esta es la secuencia:\n\n";
#print @secuencia;
#Convertir el arreglo a una variable, con el comando join.
$DNA = join('',@secuencia);
#Concatenar las líneas:
chomp @secuencia;
$DNA =~ s/\n//g; #Quita los saltos de línea.
$DNA =~ s/\s//g;

print "La secuencia original es: \n\n",$DNA,"\n\n";

#Secuencias aleatorias
$test="ACGT";
@DNA=split("",$test);

for ($j=0; $j < 100; ++$j){
    $salida="";
    for ($i=0; $i < 541; ++$i){
        $random=rand(length($test));
        $salida=$salida.$DNA[$random];
    }
    print ">Secuencia_$j\n$salida\n";
}

exit;
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Comment on Compare two variables Select or Download Code

Replies are listed 'Best First'.
Re: Compare two variables by Cristoforo (Curate) on May 19, 2014 at 22:07 UTC
This will count the matching characters. `my $orig = <DATA>; my $i = 0; while (<DATA>) { my $matches = $orig ^ $_; printf "Sequence %d has %d identities\n", $i++, $matches =~ tr/\0/ +/; } __DATA__ ATCGGGACG TCGTCAGCG ATGCGAAAA` [download] Prints: `Sequence 0 has 2 identities Sequence 1 has 4 identities` [download]	[reply] [d/l] [select]
Re^2: Compare two variables by dmunoze (Initiate) on May 20, 2014 at 00:17 UTC
Thanks for the answer, but I didn't understand the line with DATA. I mean, what exactly DATA contains?	[reply]
Re^3: Compare two variables by project129 (Beadle) on May 20, 2014 at 01:27 UTC
Hi there! Regarding data section: this is just ability to store data and executable code in one (usually small all-in-one) file, please read this short notes: perldoc.perl.org/SelfLoader.html#The-__DATA__-token	[reply]
Re^3: Compare two variables by AnomalousMonk (Archbishop) on May 20, 2014 at 14:18 UTC
Here's essentially the same thing without `__DATA__`: c:\@Work\Perl\monks>perl -wMstrict -le "my $seq = 'ATCGGGACG'; my $n = 0; ;; for my $s (qw(TCGTCAGCG ATGCGAAAA TTTTTTTTT TATTTTTTT)) { print qq{\n'$seq' original}; my $idents = (my $same = $s ^ $seq) =~ tr/\x00//; $same =~ tr/\x00-\xff/^ /; print qq{'$s' seq }, $n++; print qq{ $same $idents identities}; } " 'ATCGGGACG' original 'TCGTCAGCG' seq 0 ^^ 2 identities 'ATCGGGACG' original 'ATGCGAAAA' seq 1 ^^ ^ ^ 4 identities 'ATCGGGACG' original 'TTTTTTTTT' seq 2 ^ 1 identities 'ATCGGGACG' original 'TATTTTTTT' seq 3 0 identities [download]	[reply] [d/l] [select]
Re^3: Compare two variables by AnomalousMonk (Archbishop) on May 20, 2014 at 14:28 UTC
See also Special Literals in perldata.	[reply]
Re: Compare two variables by GotToBTru (Prior) on May 19, 2014 at 21:41 UTC
Simple way to count matching characters in two strings (assuming they are same size) `$l = length($string1); while ($l--) { $i += 1 if (substr($string1, $l, 1) eq substr($string2, $l, 1)) } print "$i identities.\n";` [download] 1 Peter 4:10	[reply] [d/l]