Perl to update field based on a specific set of rules
In the perl below, which does execute, I am having trouble with the else in Rule 3. The digit in f{8} is extracted and used to update f[55] accordinly along with the value in f[13].
There can be either - * or + before the number that is extracted but the same logic applies, that is if the value is greater than 10 and f[13] is greater than 0.01 f[55] is Likely Benign, if the value is less than 10
and f[13] is less than 0.01 f[55] is VUS in. It is possible for f[13] to be . (dot) but that is the same as zero. However, currently the value does not seem to be extracted by the perl below and I
get different output then the desired. If I comment this rule out it fixes some of the lines but causes other lines to be incorrect. I am not sure what is causing the issue or how to fix it. Thank you .
I added a description to explain each line of the output and what should be happening, which currently is not .
line 1 is Likely Benign in f[55] because in NM_001134408:exon3:c.415-43A>G in f[8] the 43 after the minus is extracted and since that value is greater than 10 f[55] is Likely Benign
line 2 is VUS in f[55] because in NM_003239:exon6:c.927-1G>C in f[8] the 1 after the minus is extracted and since that value is less than 10 and f[13] is less than 0.01 f[55] is VUS
line 3 is VUS in f[55] because in NM_001879:exon12:c.1442-5C>G in f[8] the 1 after the minus is extracted and since that value is less than 10 and f[13] is less than 0.01 f[55] is VUS
perl
Code:
# disables certain Perl expressions that could behave unexpectedly or are difficult to debug, turning them into errors
use strict;
use warnings;
# Read and display the first line of the file passed at command line.
print scalar <>;
# Read line by line the file given at the command line, could be the stdin if no file is give as argument.
while (<>)
{ # start conditional block
# Make tokens out of the line, using the tab as separator.
my @f = split /\t/;
# Select 4 tokens and define @f.
my ($FuncrefGene,$PopFreqMax,$GeneDetailrefGene,$ClinSig) = @f[6,13,8,46];
# Rule1: Default classification VUS.
my $classification = 'VUS';
# map to 0 if it doesn't have numeric meaning.
$GeneDetailrefGene = 0 if $GeneDetailrefGene eq '.';
$PopFreqMax = 0 if $PopFreqMax eq '.';
# Rule2: Change to Likely Benign if conditions occurs.
if ($PopFreqMax > 0.011) {
$classification = 'Likely Benign';
}
#Rule3: GeneDetail condition
if ($FuncrefGene !~ /exonic/i && $GeneDetailrefGene=~/^\D(\d+)$/) { # capture the digits after any non-digit into $1
if ($1 > 10) { #
$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)(\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 $transcript > 10; # Reclassify intronic variants (following c. nomenclature) to Likely Benign if distance greater than 10
}
}
# Rule4: ClinVar condition for ACMG
if ($ClinSig =~ /Pathogenic|Likely pathogenic/i) {
$classification = 'VUS';
}
# token 55 is classification.
$f[55] = $classification;
# display results and update @f.
print join "\t", @f;
} # end conditional block
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