regular expression code
- by Gaia Andreoletti
Deal all,
I need to find match between two tab delimited files files like this:
File 1:
ID1 1 65383896 65383896 G C PCNXL3
ID1 2 56788990 55678900 T A ACT1
ID1 1 56788990 55678900 T A PRO55
File 2
ID2 34 65383896 65383896 G C MET5
ID2 2 56788990 55678900 T A ACT1
ID2 2 56788990 55678900 T A HLA
what I would like to do is to retrive the matching line between the two file. What I would like to match is everyting after the gene ID
So far I have written this code but unfortunately perl keeps giving me the error:
use of "Use of uninitialized value in pattern match (m//)"
Could you please help me figure out where i am doing it wrong?
Thank you in advance!
use strict;
open (INA, $ARGV[0]) || die "cannot to open gene file";
open (INB, $ARGV[1]) || die "cannot to open coding_annotated.var files";
my @sample1 = <INA>;
my @sample2 = <INB>;
foreach my $line (@sample1) {
my @tab = split (/\t/, $line);
my $chr = $tab[1];
my $start = $tab[2];
my $end = $tab[3];
my $ref = $tab[4];
my $alt = $tab[5];
my $name = $tab[6];
foreach my $item (@sample2){
my @fields = split (/\t/,$item);
if ($fields[1]=~ m/$chr(.*)/ && $fields[2]=~ m/$start(.*)/ && $fields[4]=~ m/$ref(.*)/ && $fields[5]=~ m/$alt(.*)/&& $fields[6]=~ m/$name(.*)/){
print $line,"\n",$item;
}
}
}
