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Re^3: error calling variables? Going insane...

by poj (Monsignor)
on Jun 25, 2014 at 21:58 UTC ( #1091259=note: print w/replies, xml ) Need Help??

in reply to Re^2: error calling variables? Going insane...
in thread error calling variables? Going insane...

Forgive me if this is nonsense but if all your output is going to INTRONS_three then presumably the length of $seq is not 9. So does that mean that this block is not entered ?
if ($intron_from_boundary[$i] >= -6) { $left_of_boundary = 3; #$right_of_boundary = 6; $left_of_boundary = $left_of_boundary - intron_from_bound +ary[$i]; $new_left = 51 - $left_of_boundary; $seq = substr( $col7[$i], $new_left, 9); $matchID = $ID[$i] . "\t" . $intron_from_boundary[$i] +. "\t" . "on the negative strand"; }
Is which case is this $intron_from_boundary[$i] >= -6 the correct test, any number greater or equal to -6 ie. -5, -4, -3 etc or should it be less or equal to -6 ie -7,-8,9 etc

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Re^4: error calling variables? Going insane...
by lecb (Acolyte) on Jun 25, 2014 at 22:24 UTC

    Dear Poj,
    I have another subroutine that I call later that pulls out a sequence of length = 9, and this works absolutely fine. I have replied to suicidejunkie and have worked out the errors of my ways! - El

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