In the perl there is a default rule that sets f[55] to VUS, and then a seris of rules that will change f[55] based on the result that is
obtained from the rule. The code below is a rule that is supposed to be applicable to lines 2-4 because this rule just looks at the digit in f[8]. So in line 2 f[8] is 27
and that value is greater than 10, so f[55] would be Likely Benign. Since the symbol before the digit could be either a > or + or - in the regex I use \D to look for any non-digit before the number.
The else portion of the rule is supposed to be applicable to lines 1 and 5 as it uses the regex to parse out the digit after the - ot + or *in the string
that begins with NM_ in [ICODE] in f[8]. I am currently only getting the second line's f[55] value to be correct and I am not sure what I am doing incorrect. I have tried
changing the regex but not to the correct one (maybe there is something else I am missing). Thank you .
if ($FuncrefGene !~ /exonic/i && $GeneDetailrefGene=~/(\D\d+)/) { # capture the digits after any non-digit into $1
if ($1 > 11) { #
$1 //= 0; # Give it a value of zero if no numeric value was found.
$classification = 'Likely Benign'; # Reclassify intronic variants (with distance only) based on distance to exon > 10 to Likely Benign
}
}
else {
if ($FuncrefGene !~ /exonic/i) {
my ($transcript) = ($GeneDetailrefGene) =~ /(?:\.\d+[+*-])(\d+)/; # Get a numeric value if exists using (.) and (+/-) and capture digits into $transcript.
$transcript //= 0; # Give it a value of zero if no numeric value was found.
$classification = 'Likely Benign' if $transcript > 11; # Reclassify intronic variants (following c. nomenclature) to Likely Benign if distance greater than 10
}
}
i am using perl in win2000advanced server...
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perl -version:
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This is perl, v5.6.1 built for MSWin32-x86-multi-thread
(with 1 registered patch, see perl -V for more detail)
Copyright 1987-2001, Larry Wall
Binary build 638 provided by... (1 Reply)
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08-04-2017
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