No, it will not match because the pattern "[+*-]d=" is not present in $GeneDetailrefGene. The characters "d" and "=" do not follow any one of ("+", "*", "-").
Note that in a regex, "d" matches the character "d", but "\d" matches a single digit in the range [0-9].

Also, the stream of 1 or more digits is to be matched before [+*-].
So, you may want to use this regex:

Code:

/(?:\.\d+[+*-])(\d+)/

Code:

 ...
 ...
 I am not sure how to also use f[13} in this rule.
 ...
 ...

Just use it the way you laid down the rules in your first post.
Here's the relevant excerpt from your first post:


So, since the "value" you talk about is $transcript and f[13] is $PopFreqMax, your logic would be something like:

Code:

 if ($transcript > 10 and $PopFreqMax > 0.01) {
     $classification = "Likely Benign";
 } elsif ($transcript < 10 and $PopFreqMax < 0.01) {
     $classification = "VUS";
 }

Which you have already taken care of in line # 23 of your Perl code in your post # 1, so no worries.

I don't know why you run "Rule 2" (regarding f[13] or PopFreqMax) on its own in line # 25 through 28 of your Perl code in post # 1.

Since you have to use it in conjunction with $transcript as per your logic above, use it after you have determined the value of $transcript.


And the first one will be used, as the regex reads from the left of the string and tries to match as early as possible.

See below:

Code:

$
$ echo "NM_001134408:exon3:c.415-43A>G;NM_001134407:exon3:c.415-44A>G;NM_000833:exon4:c.415-45A>G" | perl -lne '/(?:\.\d+[+*-])(\d+)/ and print $1'
43
$
$

However, if your first "value" within $GeneDetailrefGene (where "values" are delimited by ";") does not match the pattern, then that pattern will be attempted in the second "value" within $GeneDetailrefGene.

In the example below, I have replaced the first "-" character by "#", so the pattern will not match anything in the first "value".

Code:

$
$ echo "NM_001134408:exon3:c.415#43A>G;NM_001134407:exon3:c.415-44A>G;NM_000833:exon4:c.415-45A>G" | perl -lne '/(?:\.\d+[+*-])(\d+)/ and print $1'
44
$
$

Perl keeps looking forward and extracts the first substring it encounters that matches the pattern.
This substring happens to be in the second "value" inside $GeneDetailrefGene.