in reply to match pattern from two different file

foreach my $line1(@array1)
{ 
    foreach my $line2(@array2)
        if
        {    $line1=~ /^$pattern/;
                        $line2=~ /^$pattern/;
                         $line1==$line2;
                        {  print $line1;    }
}

[download]

Your code has syntax error.

moreover eq is for comparing strings. == is for comparing numbers.

Adding code: 
#!/usr/bin/perl
use strict;
use warnings;

open(FH, "<","./file1.txt") or die "Can't Open File1\n";
open(BH, "<","./file2.txt") or die "Can't Open File2\n";

my $pattern='^LOC_Os0[1-7]g[0-9]*.[0-9]\s';

while(my $line1 = <FH>)
{
        chomp($line1);
        #print "Line1:$line1\n";
        if( $line1=~ /$pattern/)
        {
                while(my $line2 = <BH>)
                {
                        chomp($line2);

                        if($line2 =~ /$pattern/)
                        {
                                if($line1 eq $line2)
                                {
                                        print "Matches: ". $line1;
                                }
                                else
                                {
                                        print "nothing to print\n";
                                }
                        }
                }
                seek(BH,0,0);
        }
}
close(FH);
close(BH);

[download]

file1.txt

LOC_Os01g01010.1 3017 : PAS 2993,3017 : AGTAAA AAATGGAGGAATTCTGCCA
LOC_Os01g01010.2 2218 : uORF 7,129 : ATG AAGAAGACGAGACGACGACTTCCCCACTA
+GGAAACACGACGGAGGCGGAGATGATC

[download]

file2.txt

LOC_Os01g01010.1 : PS51373 HIPIP High potential iron-sulfur proteins f
+amily profile. 2139 - 2208 AATGATTTATCATGTGAGGTGAAAGA-----AGAGCACCGGG
+TGAACAGTTACACAAGAA L=-1 GAAAGTCCAAAAGCA
LOC_Os01g01010.2 : PS00022 EGF_1 EGF-like domain signature 1. 298 - 30
+9 CtCccTtcGTtC L=(-1
LOC_Os01g01010.2 2218 : uORF 7,129 : ATG AAGAAGACGAGACGACGACTTCCCCACTA
+GGAAACACGACGGAGGCGGAGATGATC

[download]
All is well

Replies are listed 'Best First'.
Re^2: match pattern from two different file
by Anonymous Monk on Jun 20, 2014 at 07:53 UTC

    thank u code but it retrieve "nothing to print" multiple times
    I also tried again by using split().but it also print same as ur code
    newly written code

    #!/usr/bin/perl
use strict;
use warnings;

open(FH, "outputps_scan_chr1_.out") or die "Can't Open File1\n";
my @array1=<FH>;
close(FH);
open(BH, "chr1_1.txt") or die "Can't Open File2\n";
my @array2=<BH>;
close(BH);
my $pat='qr/^LOC_Os0.../';

foreach my $line1(@array1)
{ 
        my @array3= split(/ /, $line1);
    foreach my $line2(@array2)
    {
        my @array4= split(/ /, $line2);        
        foreach my $line3(@array3)
            {     
        foreach my $line4(@array4)
            {    
                $line3=~ $pat;
                $line4=~ $pat;
                if ($line3 eq $line4)
                    { 
                        print $line3;    
                    }
                else 
                    {
                    print "nothing to right\n";
                    }
            }
            }
    }
}

    [download]
[reply]
[d/l]
Re^2: match pattern from two different file
by vinoth.ree (Monsignor) on Jun 20, 2014 at 08:02 UTC

    Hey do you want to match only the pattern LOC_Os0[1-7]g[0-9]+.[0-9] in each line from both the files? or entire line? As your first post matches the entire line, that why I was checking entire line match. Please correct me if i am wrong.

    All is well
[reply]
[d/l]

      yes I only want LOC_Os0[1-7]g[0-9]+.[0-9] from both files

[reply]
[d/l]

      yes I only want LOC_Os01-7g0-9+.0-9 from both files

[reply]

        Ok, then just remove the following if condition from my code and print the $line1 

        #!/usr/bin/perl
use strict;
use warnings;

open(FH, "<","./file1.txt") or die "Can't Open File1\n";
open(BH, "<","./file2.txt") or die "Can't Open File2\n";

my $pattern='^LOC_Os0[1-7]g[0-9]*.[0-9]\s';

while(my $line1 = <FH>)
{
        chomp($line1);
        #print "Line1:$line1\n";
        if( $line1=~ /$pattern/)
        {
                while(my $line2 = <BH>)
                {
                        chomp($line2);

                        if($line2 =~ /$pattern/)
                        {                                  
                            print "Matches: ". $line1;
                        }
                        else
                        {
                            print "nothing to print\n";
                        }
                        
                }
                seek(BH,0,0);
        }
}
close(FH);
close(BH);

        [download]

        All is well
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