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Full Discussion: Classify lines in file using perl
Top Forums Shell Programming and Scripting Classify lines in file using perl Post 302995619 by cmccabe on Sunday 9th of April 2017 10:58:49 AM
Old 04-09-2017
Quote:
# Rule 1. Set classification to Likely benign based on score less than 5 for exons
What would you like to happen if it is an exon but it is more than 5?
Your logic place these into rule #3 only if PopFreqMax is less than 0.011. Would these be disregarded, otherwise?
Rule 3 was meant to be a catch all type rule but maybe it is better not to have that. If Rule 1 is exon and more than 5 then the classification is VUS. So is it better to have an else statement in Rule 1 or just remove the PopFreqMax condition from Rule 3?

Quote:

# Rule 2. Reclassify intronic variants (with c.) less than 10 based on score
What would you like to happen if it is an intronic but with score more than 10?
Your logic place these into rule #3 only if PopFreqMax is less than 0.011. Do you disregard, otherwise?
I think this followss the same logic as Rule 1 in that i need an else to capture the other condition or redo Rule 3.

Quote:

# Rule 3. If none of the above tests succeeded, and the PopFreqMax < 0.011
What if the PopFreqMax is more than 0.011? Where would those go?
If PopFreqMax is greater than 0.011 classification is Likely Benign.

Quote:
Can $FuncIDPrefGene be anything else than exonic, splicing, or intronic?
Yes, these are just three of the more common, but there are several other. However eventhough there are many possible values they can all be grouped in to exonic, for exons or not exonic, for everything else.

Quote:
Would $Score ever contain a value with a plus (+12) or minor(-12)?
The number in $Score should always be 1 2 15 20 (some positive #). I used abs() just in case the format every changed to include a + or some other symbol.

Quote:
Would $Score ever contain a value beside a dot (.) that would not have a numeric interpretation?
No, a dot is only used for a null value and is always zero.

Thank you very much Smilie.
 

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