stevieP
August 24th, 2012, 03:06 AM
I have a simple question in awk, or sed or grep
suppose I want to read a file and print out every line up to and including a given expression.
Here is an example file:
HEADER IMMUNE SYSTEM 24-JUL-01 1JNJ
TITLE NMR SOLUTION STRUCTURE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: BETA2-MICROGLOBULIN;
ATOM 23 O ILE A 1 -2.899 -19.630 -3.642 1.00 0.00 O
ATOM 24 CB ILE A 1 -2.389 -22.441 -3.644 1.00 0.00 C
ATOM 32 HG13 ILE A 1 -1.569 -24.333 -4.276 1.00 0.00 H
ATOM 33 HG21 ILE A 1 -1.068 -22.119 -1.948 1.00 0.00 H
ATOM 34 HG22 ILE A 1 -0.236 -22.584 -3.448 1.00 0.00 H
ATOM 767 HB3 GLU A 47 5.674 7.664 -11.282 1.00 0.00 H
ATOM 768 HG2 GLU A 47 3.235 7.139 -11.700 1.00 0.00 H
ATOM 769 HG3 GLU A 47 2.852 8.831 -11.352 1.00 0.00 H
ATOM 770 N LYS A 48 6.056 8.485 -7.649 1.00 0.00 N
ATOM 771 CA LYS A 48 7.226 8.556 -6.785 1.00 0.00 C
ATOM 772 C LYS A 48 7.039 7.597 -5.606 1.00 0.00 C
ATOM 1630 CE MET A 99 -1.201 15.052 12.834 1.00 0.00 C
ATOM 1631 OXT MET A 99 -4.601 14.678 11.618 1.00 0.00 O
ATOM 1638 HE1 MET A 99 -2.192 15.464 12.648 1.00 0.00 H
ATOM 1639 HE2 MET A 99 -0.880 15.310 13.843 1.00 0.00 H
ATOM 1640 HE3 MET A 99 -0.497 15.471 12.117 1.00 0.00 H
TER 1641 MET A 99
ENDMDL
MODEL 2
ATOM 1 N MET A 0 -7.328 -24.381 -4.310 1.00 0.00 N
ATOM 2 CA MET A 0 -7.133 -23.021 -3.778 1.00 0.00 C
ATOM 3 C MET A 0 -6.133 -23.032 -2.619 1.00 0.00 C
ATOM 33 HG21 ILE A 1 -4.192 -25.045 -2.176 1.00 0.00 H
ATOM 34 HG22 ILE A 1 -2.597 -25.388 -1.496 1.00 0.00 H
ATOM 35 HG23 ILE A 1 -3.830 -24.623 -0.484 1.00 0.00 H
ATOM 36 HD11 ILE A 1 -2.653 -21.428 -4.153 1.00 0.00 H
suppose I want to print out everything either before "ENDMDL", or up to and including "ENDMDL"
Here is an answer:
awk 'BEGIN {flag=0;} {if (flag==0 && $1 !="ENDMDL") {print $0;} else {flag=1;}}' FILENAME
This doesn't print out the last line containing ENDMDL. It suffices for my purposes, but I also think there must be an easier awk or sed one-liner to do this, either printing out the line containing ENDMDL or not.
Thanks,
StevieP
suppose I want to read a file and print out every line up to and including a given expression.
Here is an example file:
HEADER IMMUNE SYSTEM 24-JUL-01 1JNJ
TITLE NMR SOLUTION STRUCTURE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: BETA2-MICROGLOBULIN;
ATOM 23 O ILE A 1 -2.899 -19.630 -3.642 1.00 0.00 O
ATOM 24 CB ILE A 1 -2.389 -22.441 -3.644 1.00 0.00 C
ATOM 32 HG13 ILE A 1 -1.569 -24.333 -4.276 1.00 0.00 H
ATOM 33 HG21 ILE A 1 -1.068 -22.119 -1.948 1.00 0.00 H
ATOM 34 HG22 ILE A 1 -0.236 -22.584 -3.448 1.00 0.00 H
ATOM 767 HB3 GLU A 47 5.674 7.664 -11.282 1.00 0.00 H
ATOM 768 HG2 GLU A 47 3.235 7.139 -11.700 1.00 0.00 H
ATOM 769 HG3 GLU A 47 2.852 8.831 -11.352 1.00 0.00 H
ATOM 770 N LYS A 48 6.056 8.485 -7.649 1.00 0.00 N
ATOM 771 CA LYS A 48 7.226 8.556 -6.785 1.00 0.00 C
ATOM 772 C LYS A 48 7.039 7.597 -5.606 1.00 0.00 C
ATOM 1630 CE MET A 99 -1.201 15.052 12.834 1.00 0.00 C
ATOM 1631 OXT MET A 99 -4.601 14.678 11.618 1.00 0.00 O
ATOM 1638 HE1 MET A 99 -2.192 15.464 12.648 1.00 0.00 H
ATOM 1639 HE2 MET A 99 -0.880 15.310 13.843 1.00 0.00 H
ATOM 1640 HE3 MET A 99 -0.497 15.471 12.117 1.00 0.00 H
TER 1641 MET A 99
ENDMDL
MODEL 2
ATOM 1 N MET A 0 -7.328 -24.381 -4.310 1.00 0.00 N
ATOM 2 CA MET A 0 -7.133 -23.021 -3.778 1.00 0.00 C
ATOM 3 C MET A 0 -6.133 -23.032 -2.619 1.00 0.00 C
ATOM 33 HG21 ILE A 1 -4.192 -25.045 -2.176 1.00 0.00 H
ATOM 34 HG22 ILE A 1 -2.597 -25.388 -1.496 1.00 0.00 H
ATOM 35 HG23 ILE A 1 -3.830 -24.623 -0.484 1.00 0.00 H
ATOM 36 HD11 ILE A 1 -2.653 -21.428 -4.153 1.00 0.00 H
suppose I want to print out everything either before "ENDMDL", or up to and including "ENDMDL"
Here is an answer:
awk 'BEGIN {flag=0;} {if (flag==0 && $1 !="ENDMDL") {print $0;} else {flag=1;}}' FILENAME
This doesn't print out the last line containing ENDMDL. It suffices for my purposes, but I also think there must be an easier awk or sed one-liner to do this, either printing out the line containing ENDMDL or not.
Thanks,
StevieP