Input file1:

col1    col2    col3    col4
ZGLP1   ICAM4   13.27   0.2425
ICAM4   ZGLP1   13.27   0.2425
RRP1B   CDH24   20.8    1
ZGLP1   OOEP    18.79   0.3060
ZGLP1   RRP1B   39.62   0.2972
ZGLP1   CDH24   51.21   0.2560
BBCDI   DND1    19.44   0.2833
BBCDI   SOHLH2  36.61   0.2909
DND1    SOHLH2  18      0.8

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Input file2:

chr8     18640000   18960000    ZGLP1   RRP1B   CDH24  #gene number he
+re is not fixed can be #4 #5 or more
chr8     19000000   19080000    BBCDI   DND1    SOHLH2 #gene number he
+re is not fixed can be #4 #5 or more

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I have written a code which compares col1 and col2 of file1 with each line of file2 such that, if any of the pair falls anywhere in a line of file2 then programme should print "chromosome pos1 pos2 and the matching content of the file1 with values

output file:

chr8     18640000   18960000    ZGLP1   RRP1B 39.62 0.2972
chr8     18640000   18960000    ZGLP1 CDH24 51.21   0.2560
chr8     18640000   18960000    RRP1B CDH24 20.8    1
chr8     19000000   19080000    BBCDI   DND1 19.44  0.2833
chr8     19000000   19080000    BBCDI SOHLH2 36.61  0.2909
chr8     19000000   19080000    DND1 SOHLH2 18 0.8

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so far I have tried this but it is taking so much time as my input files are huge (2gb). 

my perl code

open( AB, "file1" ) || die("cannot open");
open( BC, "file2" ) || die("cannot open");
open( OUT, ">output.txt" );

@file = <AB>;

chomp(@file);
@data = <BC>;

chomp(@data);

foreach $fl (@file) {
    if ( $fl =~ /(.*?)\s+(.*?)\s+(.*?)\s+(.*)/ ) {
        $one = $1;
        $two = $2;
        $thr = $3;
        $for = $4;
    }

    foreach $line (@data) {
        if ( $line =~ /(.*?)\s+(.*?)\s+(.*?)\s+(.*)+/ ) {
            $chr  = $1;
            $pos1 = $2;
            $pos2 = $3;
        }

        if ( $line =~ /$one/ ) {
            if ( $line =~ /$two/ ) {
                print OUT $chr, "\t", $pos1, "\t", $pos2, "\t", $fl, "
+\n";
            }
        }
    }
}

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In reply to how to speed up pattern match between two files by Anonymous Monk

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