selecting and deleting specific lines with condition
I have a set of data as below:
Quote:
HBOND SUMMARY
output to file HB_lowLyo_D_lipid_A_water_001_064.tbl,
data was sorted, intra-residue interactions are NOT included,
Distance cutoff is 4.00 angstroms, angle cutoff is 120.00 degrees
Hydrogen bond information dumped for occupancies > 0.00
Any pairs made from above numbers actually represents pairs in the 3rd and 6th field of each line in the data file.
What I want is to select the pairs from the data file made only by the numbers which are arranged at the outer most lines of the above number-molecule ordering.
To achieve this I have tried to write awk script as below to test to print out the line which I suppose to delete. But at this level I fail to select those line pairs.
Code:
#!/usr/bin/awk -f
BEGIN {
i=0
for (n=1; n<=8; n++) set[i++] = n;
for (n=57; n<=64; n++) set[i++] = n;
for (n=9; n<=49; n+=8) {set[i++] = n; set[i++] = n+7};
}
($1== "|") {
split($3, res1, "@"); split($6, res2, "@"); #print res1[1], res2[1]
if ( (res1[1] in set) == (res2[1] in set) );
{
print;
}
}
Generally, by delete one means make a new file without. I am a bit confused in trying to see the objective. It may be a multi-pass project, to collect information, rearrange it to decide what to do, and then apply those results to the original. Where did it get hard?
If you notice the first line field 3 ($3), the residue number is 59 and in filed 6, the residue number is 19. Number 59 is in the outer most line and 19 is not according to the number-molecule arrangement. So this line should NOT be deleted.
If you notice the second line, field 3 ($3), the number 19 and in filed 6 ($6) the number is 24. Number 19 is not in the outer most line but number 24 is in the outer most line. This line also should not be deleted since NOT both the numbers are in the outer most lines.
If you notice the third line, field 3 ($3), the number is 16 and filed 6 ($6) the number is 17. Since both the numbers in this pair belongs to the outer most numbers, then this line should be deleted.
So after testing the criteria of the numbers to be in the outer most lines then that line should be deleted. This is what I need to achieve and this code simply does not work as I wanted.
So, This is a negative join. Semms like his approach should be good: you need to save the outer numbers in an array, and then as you go through the lines, look them up and decide if you want to copy. You could use while read in ksh/bash and put @ in IFS to split that field into two. You could decide each number's row mathematically (( (N%8) < 2 )).
What about when field 6 and 8 do not match? No different?
Last edited by DGPickett; 09-09-2011 at 06:02 PM..
Seems to me that you could use modulus to simplify the tests.
Your number x (assumed to be less than or equal to 64?)
if x % 8 = 0 it's in the right hand column
if x % 8 = 1 it's in the left hand column
then you just have the ranges
2<=x<=7
and
58<=x<=63
---------- Post updated at 05:31 PM ---------- Previous update was at 05:03 PM ----------
Ahhh...just realized, this test is wrong!
Code:
if ( (res1[1] in set) == (res2[1] in set) );
You can't test for the value of the array element this way, only that the subscript exists!
You could set your array differently instead of using set[i++] why not
break up the array and use set[n]? Then your test should work as you would have elements as follows:
Code:
set[1] through set[8]
set[9], set[16]
set[17], set[24]
set[25], set[32]
set[33], set[40]
set[41], set[48]
set[49], set[56]
set[57] through set[64]
Two other things I noticed...remove the semicolon after the test
and change "==" to &&
Code:
if ( (res1[1] in set) && (res2[1] in set) );
This is the biggest problem your script had other than trying to
use "in" to test the set values instead of the subscripts.
This code worked for me.
Code:
#!/usr/bin/awk -f
BEGIN {
i=0
for (n=1; n<=8; n++) set[n] = n;
for (n=9; n<=49; n+=8) {
set[n] = n
set[n+7] = n+7
};
for (n=57; n<=64; n++) set[n] = n;
}
($1 == "|") {
split($3, res1, "@"); split($6, res2, "@");
if ( (res1[1] in set) && (res2[1] in set) ) # <--- no ';' here!
{
print;
}
}
Thanks so much for your kind reply. The code perfectly works now as per my need. But additionally I want to ask you something related to this. At the end of the code I write "print" so that I want to see if the code selecting the lines which I dont want exactly. Now if I want to delete those selected lines, what command should I should use?
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09-08-2011
