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should capture the 43 in NM_001134408:exon3:c.415-43A>G and that wiill be the value of $transcript?
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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:
Just use it the way you laid down the rules in your first post.
Here's the relevant excerpt from your first post:
Quote:
Originally Posted by cmccabe
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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.
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So, since the "value" you talk about is $transcript and f[13] is $PopFreqMax, your logic would be something like:
Quote:
Originally Posted by cmccabe
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It is possible for f[13] to be . (dot) but that is the same as zero.
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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.
Quote:
Originally Posted by cmccabe
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In the cases that have multiple f[8] values, like in line 1, the first can be used.
In line 1 f[8] is
NM_001134408:exon3:c.415-43A>G;NM_001134407:exon3:c.415-43A>G;NM_000833:exon4:c.415-43A>G aand the ; (semi-colon) indicates the start of a new value. NM_001134408:exon3:c.415-43A>G would be the first value, so 43 is read into the $transcript variable and since f[13] is 0.0004, f[55] is VUS. ...
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:
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".
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.
This User Gave Thanks to durden_tyler For This Post:
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