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

by bingalee (Acolyte)
on Jul 09, 2013 at 23:12 UTC ( #1043392=note: print w/replies, xml ) Need Help??


in reply to Re: find reverse complement of every 2nd line
in thread 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/;

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]; } }

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 (Chancellor) 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)

Re^3: find reverse complement of every 2nd line
by syphilis (Chancellor) 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 }
    Cheers,
    Rob

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