UNIX for Beginners Questions & Answers

Trying to use awk to format the input based on the filed count being 5. Most lines are fine using the awk below, except the first two lines. I know the reason is the -1 in green and -2 in blue. But can not figure out how to not split on the - if it is followed by a digit then letter. Thank you .

input

Code:

chr9:21971208 CDKN2A c.151-1G>A p.?
chr9:21971209 CDKN2A c.151-2A>G p.?
chr5:112175216 APC c.3925G>T p.E1309*
chr5:112175363 APC c.4072G>A p.A1358T
chr5:112175390 APC c.4099C>T p.Q1367*
EGFR,,EGFR c.2240_2257delTAAGAGAAGCAACATCTC p.L747_P753delinsS,chr7:55242470_55242487delTAAGAGAAGCAACATCTC,3470,,,,

current

Code:

chr9 21971208 CDKN2A c.151 1G>A p.?
chr9 21971209 CDKN2A c.151 2A>G p.?
chr5 112175216 112175216 APC p.E1309*
chr5 112175363 112175363 APC p.A1358T
chr5 112175390 112175390 APC p.Q1367*
chr7 55242470 55242487 EGFR c.2240_2257delTAAGAGAAGCAACATCTC p.L747_P753delinsS

desired

Code:

chr9 21971208 21971208 CDKN2A c.151-1G>A p.?
chr9 21971209 21971209 CDKN2A c.151-2A>G p.?
chr5 112175216 112175216 APC p.E1309*
chr5 112175363 112175363 APC p.A1358T
chr5 112175390 112175390 APC p.Q1367*
chr7 55242470 55242487 EGFR c.2240_2257delTAAGAGAAGCAACATCTC p.L747_P753delinsS

awk

Code:

awk -F'[ :_-]' 'NF==5{$4=$3;$3=$2} {$1=$1} 1' input

I am very confused.

The last line of your sample input contains at least 7 fields so the {$1=$1}1 should change colons, underscores, and minus signs to spaces leaving the rest of that line of input unchanged. But, instead of that, you say that you want something that replaces field 1 with the contents of the last four characters from field number 5 and rearranges lots of other parts of that input line???

Since the only minus signs in your sample input are characters that you do not want to count as field separators, why are you including them in your list of field separator characters???

Why is it that the first five lines of your output desired output don't all have the same number of fields??? If they all start out with what you want to count as five fields, shouldn't they all end up with the same number of output fields?

Please try again to explain what it is that you are trying to do and provide sample input and output that match the description of what you are trying to do!