I have a txt file (50k) proteins in it, which looks like this:
line 1:the protein code
line 2: protein length in amino acids
line 3: amino acid sequence
line 4: secondary structure
line 5: XYZ coordinates(which is numbers).
line 6:embty
the input looks like this :
4LGTD
247
M S E K L Q K V L A R A G H G S R T
. . E E H H H H H H H T T S S . H .
-34.3 -28.9 16.3 -33.0 -26.8 13.4 -29.4 -25.4 13.3 -27.9 -22.6 11.2 -26.9 -24.1 7.8 -23.3 -22.9 8.2 -23.0 -24.7 11.5 -24.1 -27.9 9.9 -21.8 -27.7 6.9 -18.8 -26.7 9.0 -19.5 -29.7 11.3 -19.6 -31.9 8.2 -16.2 -30.7 7.2 -16.7 -28.2 4.4 -15.0 -25.1 5.8 -15.4 -22.7 8.7 -18.8 -21.3 9.7 -17.7 -17.9 8.3 -16.3 -19.3 5.1 -19.5 -21.2 4.5 -21.5 -18.0 5.1 -19.7 -16.2 2.3 -20.8 -19.1 -0.0 -24.4 -19.2 1.2 -24.6 -15.4 0.6 -23.5 -16.0 -3.0 -26.4 -18.4 -3.6 -24.1 -21.4 -4.0 -25.9 -23.6 -1.5 -29.3 -25.2 -2.0 -31.4 -27.0 0.5 -34.0 -29.5 -0.8 -33.9 -27.8 -4.2 -34.1 -24.2 -3.0 -31.3 -21.7 -2.9 -30.7 -21.0 0.8 -30.2 -17.5 2.2 -27.9 -16.3 4.9 -29.4 -17.1 8.3 -31.3 -20.1 7.0 -31.7 -23.1 9.4 -32.1 -26.8 8.7 -32.6 -30.1 10.5 -30.2 -32.9 9.7 -32.0 -36.0 8.4 -31.6 -38.7 5.7 -34.0 -36.6 3.6 -32.0 -33.4 3.7 -30.4 -32.7 0.4 -27.7 -30.0 0.6 -25.8 -29.0 -2.5 -23.0 -26.6 -3.0 -22.5 -25.6 -6.6 -25.0 -28.3 -7.5 -22.9 -31.1 -5.9 -24.6 -33.1 -3.2 -23.0 -33.1 0.2 -23.1 -36.0 2.6 -23.7 -34.9 6.2 -23.8 -36.9 9.4 -27.2 -37.3 11.1 -28.5 -37.1 14.7 -19.2 -38.7 17.8 -17.7 -36.6 20.6 -14.0 -37.3 20.3 -11.2 -35.4 22.0 -7.4 -35.3 21.2 -4.7 -34.3 23.6 -1.9 -32.6 21.6 1.6 -31.6 22.7 2.2 -28.4 20.7 5.8 -27.5 20.1 7.1 -23.9 19.9 7.1 -22.6 16.3 3.6 -24.0 15.4 0.7 -21.6 14.7 -2.8 -22.2 16.0 -4.8 -21.4 12.8 -6.4 -23.3 9.9 -4.8 -20.9 7.5 -1.6 -18.8 8.1 -1.1 -16.0 5.5 2.7 -16.4 6.0 3.0 -20.1 5.2 4.2 -21.3 8.7 3.5 -24.7 10.3 0.1 -24.9 11.9 -1.1 -27.3 14.7 -3.6 -28.9 12.3 -1.0 -30.0 9.8 -0.7 -33.4 11.5 -4.0 -34.7 12.9 -6.1 -37.9 12.3 -8.5 -37.7 9.3 -12.2 -38.1 10.1 -15.3 -39.0 8.2 -17.5 -36.0 7.6 -16.2 -34.0 10.6 -13.2 -31.8 11.6 -10.9 -31.0 14.5 -11.7 -27.8 16.4 -8.8 -26.3 18.5 -9.8 -25.6 22.1 -8.4 -22.1 22.1 -5.0 -20.9 20.9 -1.5 -21.1 22.2 1.2 -18.6 21.2 3.8 -19.7 18.6 6.6 -20.0 21.1 4.5 -21.3 23.9 4.7 -25.1 24.5 2.3 -27.7 25.8 -1.3 -29.0 25.9 -3.8 -28.1 23.2 -7.0 -30.0 23.1 -8.9 -30.7 19.9 -12.5 -32.0 19.6 -14.9 -32.8 16.9 -17.6 -31.5 19.2 -17.9 -27.7 18.8 -20.2 -27.3 21.8 -17.6 -29.0 24.0 -15.0 -26.8 22.4 -16.8 -23.5 23.1 -17.7 -24.6 26.6 -14.1 -25.3 27.4 -12.9 -21.9 26.0 -15.6 -19.6 27.2 -14.8 -18.2 30.6 -18.4 -18.5 31.9 -17.5 -22.1 32.5 -14.3 -21.2 34.4 -12.2 -24.1 33.1 -8.7 -24.1 34.5 -5.7 -23.6 32.3 -2.5 -24.5 34.2 0.9 -23.2 33.2 4.4 -23.9 34.3 6.1 -20.6 34.0 9.8 -20.0 34.3 10.1 -16.4 35.4 13.0 -14.0 35.5 13.3 -11.2 38.1 12.7 -10.5 41.8 9.7 -12.2 43.3 8.4 -12.0 46.8 5.2 -13.0 48.6 3.7 -9.5 48.4 3.8 -9.8 44.6 2.2 -13.2 44.8 -0.6 -11.7 47.0 -1.0 -8.9 44.5 -1.3 -11.3 41.5 -3.9 -13.4 43.4 -6.1 -10.5 44.4 -6.1 -8.6 41.1 -3.9 -6.2 39.3 -4.5 -3.7 36.4 -3.6 -4.8 32.9 -3.8 -2.6 29.8 -7.0 -4.4 29.0 -8.5 -4.4 32.5 -8.2 -6.2 35.8 -6.8 -9.7 35.9 -5.7 -12.2 38.6 -4.2 -15.6 38.7 -6.6 -18.1 40.2 -3.8 -20.0 41.8 -0.0 -19.4 42.0 2.4 -21.9 43.4 6.2 -21.7 43.7 7.6 -24.7 41.8 11.4 -24.5 42.2 14.2 -22.0 42.2 17.4 -20.5 41.0 18.6 -17.0 41.7 16.7 -14.6 39.4 15.1 -17.6 37.8 12.2 -19.4 39.4 9.4 -21.8 38.3 5.8 -21.1 39.2 2.7 -23.1 38.4 -0.3 -20.8 37.8 -3.8 -21.1 36.7 -6.3 -18.9 34.9 -9.9 -19.4 34.1 -9.9 -17.1 31.1 -7.6 -16.7 28.1 -6.8 -13.1 27.2 -4.0 -12.5 24.7 -0.6 -13.1 26.3 -2.2 -12.9 29.7 0.3 -14.9 31.8 3.2 -12.8 30.5 1.3 -9.5 31.1 0.4 -10.5 34.6 4.0 -11.2 35.6 5.1 -8.0 33.8 2.5 -6.0 35.8 4.6 -6.8 38.9 8.0 -6.3 37.2 8.8 -9.9 36.2 9.7 -11.4 32.9 8.9 -14.8 31.5 11.6 -17.1 30.0 9.5 -20.2 29.5 5.8 -21.0 29.3 4.3 -24.5 29.1 0.6 -25.3 29.3 0.5 -28.5 31.4 -3.2 -28.9 32.0 -6.5 -27.9 30.5 -9.5 -28.7 32.7 -9.1 -32.2 34.0 -6.7 -33.3 31.2 -3.0 -32.9 32.1 -0.4 -33.0 29.4 -0.1 -36.8 28.8 2.9 -38.3 30.7 4.2 -40.6 28.0 3.5 -38.2 25.2 6.4 -36.4 23.5 6.5 -32.9 22.0 4.6 -32.8 18.6 2.5 -35.9 19.2 -1.1 -36.5 20.3 -3.4 -39.1 21.9 -7.1 -39.7 22.0 -9.2 -39.8 25.2 -11.5 -42.8 25.8 -15.2 -42.7 26.7 -14.8 -42.3 30.4 -12.3 -39.5 30.0 -14.2 -37.7 27.3 -17.3 -38.0 29.6 -15.4 -36.5 32.6 -14.3 -33.6 30.4 -17.9 -33.1 29.4 -19.2 -33.2 33.0 -16.7 -30.4 33.8 -18.7 -28.1 31.6 -22.2 -29.4 32.6 -22.6 -31.6 29.5 -24.2 -35.0 30.3 -22.3 -38.2 29.6 -22.5 -39.9 26.3 -22.8 -43.7 25.4
1XXIJ
334
M R W Y P W L R P D F E K L V A S L
. . . . T T H H H H H H H H H T T .
65.7 -16.7 128.5 64.5 -19.9 130.3 66.9 -22.7 131.5 66.0 -25.8 129.7 67.1 -29.4 130.9 69.2 -30.4 127.8 71.4 -27.4 128.6 72.9 -29.3 131.5 75.3 -32.0 130.1 76.9 -29.2 128.1 76.9 -26.7 131.0 78.6 -29.4 133.1 81.8 -29.7 131.1 81.8 -26.0 130.4 82.2 -25.2 134.1 84.3 -28.3 134.6 87.0 -26.5 132.5 86.5 -23.1 134.2 87.2 -24.8 137.5 90.3 -26.9 136.4 91.9 -24.1 134.3 91.2 -25.8 130.9 88.8 -22.9 130.1 88.9 -21.4 126.6 89.0 -17.6 126.7 86.9 -17.5 123.5 83.8 -19.6 123.0 81.6 -19.9 119.9 78.4 -21.8 120.5 76.4 -23.0 117.5 72.8 -23.9 117.9 69.4 -23.9 116.3 66.9 -21.3 117.2 65.1 -21.8 120.5 67.7 -24.4 121.7 68.4 -22.5 124.8 71.4 -20.9 123.2 70.2 -17.9 125.1 70.3 -19.4 128.5 73.6 -21.3 128.3 75.7 -18.2 127.8 74.1 -16.3 130.7 74.1 -19.4 133.0 77.8 -19.8 132.3 78.8 -16.2 133.0 77.0 -16.2 136.4 79.4 -18.9 137.5 82.4 -16.9 136.6 81.1 -13.6 138.0 80.6 -14.9 141.5 82.7 -13.6 144.4 81.9 -16.6 146.7 80.7 -19.6 144.5 79.2 -22.6 146.2 80.7 -25.3 143.9 78.7 -25.6 140.7 76.6 -22.5 141.0 76.6 -19.1 142.8 75.6 -18.0 146.3 73.1 -15.2 145.4 74.5 -12.7 148.0 78.0 -11.6 146.9 78.5 -8.3 145.0 78.7 -10.2 141.8 75.6 -12.3 142.3 73.7 -9.2 143.5 74.8 -6.8 140.8 74.2 -9.8 138.5 70.6 -10.2 139.7 70.4 -6.4 139.2 71.7 -7.1 135.7 74.0 -4.0 135.8 77.6 -5.1 136.4 81.1 -3.7 135.7 82.4 -7.0 134.2 79.5 -8.2 132.2 79.4 -6.7 128.7 76.5 -7.3 126.2 77.5 -6.8 122.6 74.1 -6.4 121.0 74.1 -5.1 117.4 73.4 -1.3 116.8 69.7 -0.7 117.7 67.9 -0.2 114.4 70.3 -1.8 112.0 70.7 -5.6 111.3 74.4 -5.6 111.8 77.1 -4.7 114.4 79.7 -1.9 114.3 83.5 -1.7 114.3 82.9 1.0 117.0 81.1 -1.0 119.7 83.9 -3.6 119.5 86.8 -1.2 119.9 85.1 0.5 122.9 84.7 -2.8 124.7 88.3 -3.9 123.7 89.8 -0.9 125.5 87.2 -1.3 128.2 88.8 -4.6 129.1 92.3 -3.2 128.8 91.9 -1.8 132.3 91.6 -3.7 135.7 88.3 -5.5 136.6 86.3 -3.2 138.9 85.3 -6.1 141.2 88.7 -7.8 141.0 88.2 -11.1 139.2 87.1 -12.3 135.8 85.6 -10.1 132.9 83.1 -11.6 130.4 81.8 -10.7 126.9 78.9 -12.0 124.9 77.8 -11.6 121.3 74.2 -12.0 120.1 75.2 -13.4 116.7 78.7 -13.1 115.2 77.5 -13.8 111.7 75.7 -10.4 111.7 78.8 -8.2 112.1 80.6 -5.9 109.6 83.7 -7.5 107.9 85.8 -4.8 109.5 84.2 -5.5 112.9 85.6 -9.1 112.6 89.2 -8.1 112.3 88.8 -5.4 114.9 87.8 -8.1 117.3 90.6 -10.6 116.4 93.6 -8.6 117.7 92.2 -8.7 121.2 91.9 -12.5 121.2 95.5 -12.5 120.1 96.5 -10.2 123.0 94.2 -11.8 125.7 93.9 -9.5 128.8 94.7 -11.9 131.7 91.7 -13.9 133.1 89.1 -12.4 130.8 86.3 -14.5 129.1 84.5 -14.4 125.7 81.3 -15.9 124.4 80.5 -15.9 120.7 77.3 -17.4 119.5 76.0 -18.2 116.0 73.5 -20.3 114.2 75.8 -20.6 111.2 79.5 -20.8 112.0 80.6 -21.2 108.4 79.5 -17.8 107.3 82.1 -16.6 109.9 85.7 -15.6 109.1 87.9 -18.7 109.1 90.7 -16.8 110.8 88.2 -15.8 113.5 86.5 -19.2 114.1 90.0 -20.6 114.6 90.7 -18.5 117.7 87.6 -19.7 119.5 86.5 -23.1 120.6 83.4 -24.2 118.7 80.9 -26.1 120.8 77.9 -27.9 119.3 74.6 -27.5 121.1 73.0 -30.7 119.6 69.2 -30.8 118.8 68.0 -33.4 121.2 66.8 -36.7 119.7 63.3 -36.2 118.3 61.6 -38.6 120.7 62.8 -36.6 123.6 61.9 -33.2 122.0 58.4 -34.3 121.2 57.6 -35.6 124.7 59.0 -32.4 126.2 56.8 -30.5 123.8 53.6 -32.5 124.5 53.8 -30.9 127.9 54.2 -27.3 126.9 51.2 -27.5 124.5 48.6 -30.1 123.9 48.5 -30.9 120.2 48.7 -34.1 118.1 52.2 -35.6 118.2 52.1 -35.5 114.4 51.8 -31.8 114.5 54.3 -31.6 117.3 56.9 -33.4 115.1 56.1 -31.1 112.2 56.9 -28.0 114.3 60.2 -29.7 115.5 61.2 -30.5 111.9 60.2 -27.0 110.8 62.8 -25.7 113.3 65.7 -27.9 112.4 65.1 -29.8 115.6 65.1 -26.7 117.9 62.5 -27.5 120.5 62.4 -23.9 121.6 61.6 -22.5 118.2 59.2 -25.4 117.7 57.4 -24.4 120.9 57.2 -20.8 119.7 55.7 -22.0 116.5 52.5 -22.6 118.4 52.3 -19.7 120.9 51.0 -17.2 118.3 48.2 -18.8 116.5 50.9 -19.8 114.0 50.0 -23.4 113.8 46.4 -22.5 113.1 47.8 -20.1 110.4 49.7 -23.1 109.1 46.6 -25.3 109.0 45.0 -22.6 106.8 47.8 -23.0 104.4 47.6 -26.8 104.0 43.8 -26.5 103.4 44.3 -24.0 100.7 47.1 -26.1 99.2 44.9 -29.2 99.2 42.3 -27.4 97.2 44.7 -26.0 94.7 46.9 -29.1 94.1 44.1 -31.1 92.5 42.2 -28.1 91.1 45.1 -26.2 89.4 43.8 -22.9 90.9 47.0 -22.0 92.7 46.0 -18.4 92.8 43.6 -19.4 95.6 46.6 -19.4 98.0 46.7 -15.7 97.7 44.6 -15.2 100.8 46.6 -17.8 102.7 50.0 -16.3 101.8 49.4 -12.6 101.4 50.1 -11.5 104.9 53.0 -9.8 106.8 54.0 -13.4 107.8 54.5 -14.0 104.1 58.1 -15.2 104.4 57.5 -17.6 107.2 54.6 -18.9 105.2 56.4 -19.2 101.9 59.0 -21.3 103.7 56.2 -23.6 105.0 55.0 -24.0 101.4 58.6 -24.8 100.4 59.0 -27.6 102.9 56.0 -29.3 101.4 57.5 -28.8 97.9 60.7 -30.3 99.0 59.0 -33.4 100.5 57.0 -34.1 97.3 60.3 -33.9 95.5 62.0 -36.3 97.9 59.2 -38.8 97.5 59.9 -39.0 93.7 63.3 -40.3 94.6 61.9 -42.6 97.2 63.3 -40.7 100.2 62.2 -42.2 103.5 62.3 -39.0 105.6 59.6 -36.3 105.3 59.3 -33.1 107.2 55.6 -32.7 106.8 54.4 -35.9 108.5 51.5 -33.8 109.6 49.8 -34.3 106.2 51.3 -37.2 104.2 48.2 -37.2 102.1 49.2 -33.8 100.8 52.8 -34.5 99.9 51.5 -37.6 98.1 48.9 -36.0 95.9 51.3 -33.1 95.3 54.0 -35.5 94.1 51.3 -37.3 92.0 50.2 -34.2 90.0 53.6 -32.6 89.7 56.6 -34.0 87.9 59.9 -33.8 89.7 60.9 -31.0 87.3 57.8 -28.9 87.8 58.3 -29.2 91.5 62.0 -28.0 91.2 60.8 -25.0 89.2 58.2 -24.0 91.7 60.5 -24.7 94.7 62.8 -22.0 93.4 60.4 -19.2 92.5 58.9 -19.8 95.9 62.4 -19.6 97.2 63.7 -16.5 95.4 60.4 -14.7 95.9 60.3 -15.3 99.6 63.7 -13.7 99.7 62.8 -10.5 97.9 60.1 -10.1 100.5 62.5 -10.4 103.3 65.4 -8.5 101.8 64.0 -5.6 99.5 62.8 -2.7 101.7 59.2 -2.6 100.6 57.9 -4.3 97.4 54.2 -5.0 96.9 53.5 -8.2 98.9 50.4 -8.5 96.9 51.8 -8.1 93.4 54.8 -10.2 93.8 52.9 -13.1 95.2 50.1 -12.8 92.6 52.9 -13.0 90.1 54.5 -16.0 91.9 51.1 -17.7 91.9 50.0 -17.1 88.3 53.5 -18.0 87.3 53.3 -21.3 89.1 50.3 -22.1 87.0 52.1 -21.6 83.7 54.8 -24.0 84.7 52.0 -26.5 85.2 50.8 -26.1 81.6 52.0 -28.7 79.0 54.8 -27.5 76.7 56.2 -24.8 78.9 60.0 -24.6 79.4 60.6 -24.0 83.1 63.6 -22.0 84.5 67.2 -23.0 85.4 69.4 -21.4 88.1 71.8 -18.6 87.1 75.6 -17.8 87.3
and so on (the same structure)
Please note in line 5; There is a space between x and y and y and z, but each XYZ group is tab-separated from the next.
Now I am unsure if the code down works and computing the distance between ( XYZ coordinates) correctly or not!
awk '
NR%6==5 { printf "%f\n", sqrt(($1-x)^2 + ($2-y)^2 + ($3-z)^2) }
{ x=$1; y=$2; z=$3 }' myfile.adataset
But I want the output to be like this, which is to print also the lines 1,2,3,4 , and the results:
4LGTD
247
M S E K L Q K V L
. . E E H H H H H
the result
1XXIJ
334
M R W Y P W L R P
T T H H H H H
the result
and so on
So after that, I want other code to delete blocks of lines(1,2,3,4,5)if the results of XYZ coordinates are bigger than (4.5)? Any suggestions code for first computing the distance and then deleting if the line 5 result is bigger than 4.5 by awk to do this?
NR%5==5
condition is always false.NR%5
is always between 0 and 4 $\endgroup$$1
,$2
and$3
never works fine $\endgroup$awk
command, columns are (by default) separated by space or tabulation $\endgroup$