Deleting lines with sed or awk

Question

I have a file data.txt like this.

>1BN5.txt
207
208
211
>1B24.txt
88
92

I have a folder F1 that contains text files.

1BN5.txt file in F1 folder is shown below.

ATOM    421  CA  SER A 207      68.627 -29.819   8.533  1.00 50.79           C 
ATOM    421  CA  SER A 207      68.627 -29.819   8.533  1.00 50.79           C  
ATOM    422  C   SER A 248      70.124 -29.955   8.226  1.00 55.81           C 
ATOM    615  H   LEU B 208       3.361  -5.394  -6.021  1.00 10.00           H
ATOM    616  HA  LEU B 211       2.930  -4.494  -3.302  1.00 10.00           H 
ATOM    626  N   MET B  87       1.054  -3.071  -5.633  1.00 10.00           N  
ATOM    627  CA  MET B  87      -0.213  -2.354  -5.826  1.00 10.00           C 

1B24.txt file in F1 folder is shown below.

ATOM    630  CB  MET B  87      -0.476  -2.140  -7.318  1.00 10.00           C 
ATOM    631  CG  MET B  88      -0.828  -0.688  -7.575  1.00 10.00           C
ATOM    632  SD  MET B  88      -2.380  -0.156  -6.830  1.00 10.00           S
ATOM    643  N   ALA B  92      -1.541  -4.371  -5.366  1.00 10.00           N  
ATOM    644  CA  ALA B  94      -2.560  -5.149  -4.675  1.00 10.00           C

I need only the lines containing 207,208,211(6th column)in 1BN5.txt file. I want to delete other lines in 1BN5.txt file. Like this, I need only the lines containing 88,92 in 1B24.txt file.

Desired output

1BN5.txt file

ATOM    421  CA  SER A 207      68.627 -29.819   8.533  1.00 50.79           C
ATOM    421  CA  SER A 207      68.627 -29.819   8.533  1.00 50.79           C 
ATOM    615  H   LEU B 208       3.361  -5.394  -6.021  1.00 10.00           H  
ATOM    616  HA  LEU B 211       2.930  -4.494  -3.302  1.00 10.00           H

1B24.txt file

ATOM    631  CG  MET B  88      -0.828  -0.688  -7.575  1.00 10.00           C
ATOM    632  SD  MET B  88      -2.380  -0.156  -6.830  1.00 10.00           S
ATOM    643  N   ALA B  92      -1.541  -4.371  -5.366  1.00 10.00           N 

Answer 1

Here's one way using GNU awk. Run like:

awk -f script.awk data.txt

Contents of script.awk:

/^>/ {
    file = substr($1,2)
    next
}

{
    a[file][$1]
}

END {

    for (i in a) {

        while ( ( getline line < ("./F1/" i) ) > 0 ) {

            split(line,b)

            for (j in a[i]) {

                if (b[6]==j) {

                    print line > "./F1/" i ".new"
                }
            }
        }

        system(sprintf("mv ./F1/%s.new ./F1/%s", i, i))
    }
}

Alternatively, here's the one-liner:

awk '/^>/ { file = substr($1,2); next } { a[file][$1] } END { for (i in a) { while ( ( getline line < ("./F1/" i) ) > 0 ) { split(line,b); for (j in a[i]) if (b[6]==j) print line > "./F1/" i ".new" } system(sprintf("mv ./F1/%s.new ./F1/%s", i, i)) } }' data.txt

---

---

If you have an older version of awk, older than GNU Awk 4.0.0, you could try the following. Run like:

awk -f script.awk data.txt

Contents of script.awk:

/^>/ {
    file = substr($1,2)
    next
}

{
    a[file]=( a[file] ? a[file] SUBSEP : "") $1
}

END {

    for (i in a) {

        split(a[i],b,SUBSEP)

        while ( ( getline line < ("./F1/" i) ) > 0 ) {

            split(line,c)

            for (j in b) {

                if (c[6]==b[j]) {

                    print line > "./F1/" i ".new"
                }
            }
        }

        system(sprintf("mv ./F1/%s.new ./F1/%s", i, i))
    }
}

Alternatively, here's the one-liner:

awk '/^>/ { file = substr($1,2); next } { a[file]=( a[file] ? a[file] SUBSEP : "") $1 } END { for (i in a) { split(a[i],b,SUBSEP); while ( ( getline line < ("./F1/" i) ) > 0 ) { split(line,c); for (j in b) if (c[6]==b[j]) print line > "./F1/" i ".new" } system(sprintf("mv ./F1/%s.new ./F1/%s", i, i)) } }' data.txt

---

---

Please note that this script does exactly as you describe. It expects files like 1BN5.txt and 1B24.txt to reside in the folder F1 in the present working directory. It will also overwrite your original files. If this is not the desired behavior, drop the system() call. HTH.

Results:

Contents of F1/1BN5.txt:

ATOM    421  CA  SER A 207      68.627 -29.819   8.533  1.00 50.79           C 
ATOM    421  CA  SER A 207      68.627 -29.819   8.533  1.00 50.79           C  
ATOM    615  H   LEU B 208       3.361  -5.394  -6.021  1.00 10.00           H
ATOM    616  HA  LEU B 211       2.930  -4.494  -3.302  1.00 10.00           H 

Contents of F1/1B24.txt:

ATOM    631  CG  MET B  88      -0.828  -0.688  -7.575  1.00 10.00           C
ATOM    632  SD  MET B  88      -2.380  -0.156  -6.830  1.00 10.00           S
ATOM    643  N   ALA B  92      -1.541  -4.371  -5.366  1.00 10.00           N

Answer 2

Don't try to delete lines from the existing file, try to create a new file with only the lines you want to have:

cat 1bn5.txt | awk '$6 == 207 || $6 == 208 || $6 == 211 { print }' > output.txt