delete rows after specific character | awk - bash

Question

I am writing a Bash script and,
I need to remove all lines in between TER, including 'TER's
Input File :
ATOM 186 O3' U 6 7.297 6.145 -5.250 1.00 0.00 O
ATOM 187 HO3' U 6 7.342 5.410 -5.865 1.00 0.00 H
TER
ATOM 1 HO5' A 1 3.429 -7.861 3.641 1.00 0.00 H
ATOM 2 O5' A 1 4.232 -7.360 3.480 1.00 0.00 O
ATOM 3 C5' A 1 5.480 -8.064 3.350 1.00 0.00 C
ATOM 4 H5' A 1 5.429 -8.766 2.518 1.00 0.00 H
TER
Expected output:
ATOM 186 O3' U 6 7.297 6.145 -5.250 1.00 0.00 O
ATOM 187 HO3' U 6 7.342 5.410 -5.865 1.00 0.00 H
I found
sed '/TER/,$d' ${myArray[j]}.txt >> ${MyArray[j]}.txt ### ${MyArray[j]} file name through an array
But this does not work, I think awk will work with Bash Script. help Thanks

Answer 1

You can just use sed like this:
sed -i.bak '/^TER/,/^TER/d' "${myArray[j]}.txt"
cat "${myArray[j]}.txt"
ATOM 186 O3' U 6 7.297 6.145 -5.250 1.00 0.00 O
ATOM 187 HO3' U 6 7.342 5.410 -5.865 1.00 0.00 H

Answer 2

sed '/TER/,/TER/d'
echo
"ATOM 186 O3' U 6 7.297 6.145 -5.250 1.00 0.00 O
ATOM 187 HO3' U 6 7.342 5.410 -5.865 1.00 0.00 H
TER
ATOM 1 HO5' A 1 3.429 -7.861 3.641 1.00 0.00 H
ATOM 2 O5' A 1 4.232 -7.360 3.480 1.00 0.00 O
ATOM 3 C5' A 1 5.480 -8.064 3.350 1.00 0.00 C
ATOM 4 H5' A 1 5.429 -8.766 2.518 1.00 0.00 H
TER" |sed '/TER/,/TER/d'
######################################################################################
ATOM 186 O3' U 6 7.297 6.145 -5.250 1.00 0.00 O
ATOM 187 HO3' U 6 7.342 5.410 -5.865 1.00 0.00 H
sed '/Start Pattern/,/End Pattern/d'

Answer 3

It can be done like this
sed '/TER/,$d' ${myArray[j]}.txt > tmp.txt #note only one " > "
mv tmp.txt ${myArray[j]}.txt

Answer 4

awk also provides a simple solution using a flag to control printing. Below the skip variable is used as a flag. If 1 the lines are skipped, on the transition from 1 to 0, the script exits.
awk -v skip=0 '$1=="TER"{skip=skip?1:0; if (!skip)exit}1' file
Above $1=="TER" is used to match lines (records) where the first field is TER (this disambiguates between "TER" and "TERMINAL", etc...) Within the rule, the ternary skip=skip?1:0 sets skip=1 the first time "TER" is encountered and to 0 on the next. If skip==0 the script exits. The 1 at the end is just shorthand for print.
Example Use/Output
Using your data in file, you would get:
$ awk -v skip=0 '$1=="TER"{skip=skip?1:0; if (!skip)exit}1' file
ATOM 186 O3' U 6 7.297 6.145 -5.250 1.00 0.00 O
ATOM 187 HO3' U 6 7.342 5.410 -5.865 1.00 0.00 H