ok. Please consider again the input files, with both candidates, for E and M as well.
File 1
chr7 151046672
chr7 151047369
chr3 127680920
chr3 127680920
File 2
chr1 66953622 66953654
chr1 67200451 67200472
chr1 67200475 67200478
chr1 67058869 67058880
chr1 67058881 67058885
chr7 151046672 127680920
chr7 151047369 127680920
chr3 127680920 151046672
chr3 127680920 151047369
Code for now.
#!/usr/bin/perl
use warnings;
use strict;
use Data::Dumper;
my $file1 = $ARGV[0];
open($infile1,$file1);
my $file2 = $ARGV[1];
open($infile2,$file2);
my %file2_hash;
while (my $line = <$infile1>)
{
chomp $line; #so that output with E or M can be on same line
next if $line =~ /^\s*$/; #skip blank lines (a common infile goof
+)
my ($chr, $val1, $val2) = split /\s+/,$line;
}
close $infile1;
while (my $line = <$infile2>)
{
chomp $line;
next if $line =~ /^\s*$/; #skip blank lines (a common infile goof)
my ($key, $value1, $value2) = split /\s+/, $line; # use better "nam
+es" I have
# no idea of what a chr col
$file2_hash{"$key:$value1:$value2"} = 1;
# file handle closure is optional, but I'd do it.
### process each line in file2:
### If a line "matches" with any line in file1, then "E", else "M"
### I don't know that these numbers mean, come up with better comment
close $infile2;
if (exists $file2_hash{"$chr:$val1:$val2"})
{
print "$line\tE\n"; # match exists with file 1
}
else
{
print "$line\tM\n"; # match does NOT exist with file 1
}
}
Its not working, Since I want to print the output with respect to my file 1. If you can help with. I Know there is some error in 'If' statement. I could note understand that..
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