Bash function to suppress warning message for specific text and display prompt
In the below bash function multiple variants are input and stored in a variable $variant, and each is written to an out file at c:/Users/cmccabe/Desktop/Python27/out.txt stored on a separate line.
contents of out.txt
Each individual variant then goes through functions nomenclature, check, and convert.
The bash below runs as is, but I need to modify it to account for if a line in variant has a +/- in it (like line 1 does, NM_003924.3:c.242-1G>A).
The +/- always occurs in the same location (that is right before the last number in the c. and first letter before the > in the line but can vary in the amount of digits.
After the nomenclature function runs a out_name.txt is created at C:/Users/cmccabe/Desktop/Python27/out_name.txt and looks like the below:
I am trying to add a condition that will suppress the warning message $2 for the line in bold.
In addition, that line "is an intronic variant" is displayed. My attempt to incorporate these changes is below in bold, I hope it is a start. I apologize for the long post, just trying to include enough detail. Thank you .
moderator please close as i am going to repost a cleaner thread. Thank you.
Last edited by cmccabe; 03-09-2017 at 12:53 PM..
Reason: added moderator comment
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