delete rows after specific character | awk

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

Appending to the same file you're reading is not the best idea. — Shawn, Mar 06 '20 at 17:45
expeced output is first two line, without line between TER ...... TER — Hutch, Mar 06 '20 at 17:45
The `sed` script `'/TER/,$d` by itself generates the correct output (even though it would delete also the lines following the second `TER`). But as @Shawn suggested, the problem in you original command is another. — Enlico, Mar 06 '20 at 18:02
Does this answer your question? [Using sed to delete all lines between two matching patterns](https://stackoverflow.com/questions/6287755/using-sed-to-delete-all-lines-between-two-matching-patterns) — Sorin, Mar 06 '20 at 19:05
@shawn you are right, changing the file name solved the problem, also append, only ">" I should use, I would do it like this ${myArray[j]}.txt >> a.txt , in next command, mv a.txt > ${myArray[j]}.txt Thanks — Hutch, Mar 06 '20 at 19:16

score 0 · Answer 1 · answered Mar 06 '20 at 18:00

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

score 0 · Accepted Answer · edited Mar 07 '20 at 23:24

0

It can be done like this

sed '/TER/,$d' ${myArray[j]}.txt > tmp.txt #note only one " > "
mv tmp.txt ${myArray[j]}.txt

edited Mar 07 '20 at 23:24

Bhargav Rao

50,140
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answered Mar 06 '20 at 19:24

Hutch

167
2
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score 0 · Answer 3 · answered Mar 07 '20 at 11:24

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'

Better anchored as `sed '/^\s*TER$/,/^\s*TER$/d'` to require `TER` as the first non-whitespace word and disambiguating from `TERMINAL`, etc.. — David C. Rankin, Mar 08 '20 at 01:38

score 0 · Answer 4 · answered Mar 08 '20 at 01:50

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

delete rows after specific character | awk

4 Answers4