Re^2: find reverse complement of every 2nd line

Hey Dave. For the reverse complement the code will be something like this

my $raw=<IN>;
$rev= reverse $raw;
$rev=~tr/ATGCatgc/TACGtacg/;
[download]

my problem actually is doing this only to every other line and not the entire file

this is what i came up with, but it doesnt work

while(@inf=<IN>)
{
 if(i%2==1)
{
$inf[i]=reverse $inf[i];
}
}
[download]

In this i was just trying to find the reverse to see if this code performs the action on the lines I want it to.. but no luck. Im still thinking of any other way. Any suggestions?

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Re^3: find reverse complement of every 2nd line by LanX (Saint) on Jul 09, 2013 at 23:27 UTC
variables in Perl need sigils, so it must be `$i` not just `i` (using strict and warnings should have prevented you) and you need to increment it with `++$i` within the loop. As an alternative you could just test `$. % 2` since `$.` automatically holds the line-number. Cheers Rolf ( addicted to the Perl Programming Language)	[reply] [d/l] [select]
Re^3: find reverse complement of every 2nd line by syphilis (Archbishop) on Jul 09, 2013 at 23:40 UTC
my problem actually is doing this only to every other line and not the entire file The special variable `$.` (documented in `perldoc perlvar`) keeps count of the line numbers, so you can do something like: `while(<IN>) { next if $. % 2; # skip odd lines # do the processing }` [download] Cheers, Rob	[reply] [d/l] [select]