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?

In reply to Re^2: find reverse complement of every 2nd line by bingalee
in thread find reverse complement of every 2nd line by bingalee

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