Linux

hii
i have a file that contains lines like this

4829:71370 1:N:0:CGATGT + chr6 126912761 GAAGGCATAGCCCGTTGGGCTGTGGTCATCAGCCTC CCCFFFFFHGHHHJHIJJJHIJIGHCGIIJJJJIJI 0 4829:71370 2:N:0:CGATGT + chr7 89349071 AGCCCTGCCCCCACCCCCCATTCTTCTTGACTGTCT C@@FFFFFHHHGHJ
JIJIJIIIIJJJJJJJJIIJIJ 0

Now i want to check whether chr6 presently at 3rd position is matching with the other chr7 at 11nth (in this line). with my perl script fails as positions change for other lines. any way to do this.

Is "chrX" always preceded by "+"? BTW this thread should be posted in "Shell Programming and Scripting"

ya "chrx" is preceeded by either + 0r -
i am sorry for wrong post.

Try:

Code:

perl -nle 'if(/(\+\s+chr\d).*(\+\s+chr\d)/){if($1 eq $2){print "line $.: match"}else{print "line $.: no match"}}' file

hiii
thanks alot. just nw solved it


my @cmp = $line[$i] =~ /\tchr([0-9]+)\t/g;
if (2 == @cmp and $cmp[0] != $cmp[1]) {
print $line[$i];