I have two files and would like to find out which parts of file 1 occur in the same order/sequence of file 2 based on one of multiple columns (col4). The files are sorted based on an identifier in col1 (from 1 to n) but the identifier is not the between the files. The column in file 1 always occurs as one block in file 2.
file1:
x 1
x 2
x 3
file2:
y 5
y 1
y 2
y 3
y 6
output:
y 1
y 2
y 3
Another thing to take into consideration is, that the entries in the column to be filtered on are not unique.
I already tried
awk 'FNR==NR{ a[$2]=$2;next } ($2 in a)' file1 file2 > output
but it only works if you have unique identifiers.
To clarify it with real life data: I would like to extract the rows where I have the same order based on column 4.
File1:
ATOM 13 O ALA A 2 37.353 35.331 -19.903 1.00 71.02 O
ATOM 18 O TRP A 3 38.607 32.133 -18.273 1.00 69.13 O
File2:
ATOM 1 N MET A 1 42.218 38.990 -18.511 1.00 64.21 N
ATOM 10 CA ALA A 2 38.451 37.475 -20.033 1.00 71.02 C
ATOM 13 O ALA A 2 37.353 35.331 -19.903 1.00 71.02 O
ATOM 18 O TRP A 3 38.607 32.133 -18.273 1.00 69.13 O
ATOM 29 CA ILE A 4 38.644 33.633 -15.907 1.00 72.47 C
Related
I have the following data:
a b c d
5 9 6 0
3 1 3 2
Characters in the first row, numbers in the second row.
How do I get the character corresponding to the highest number in the second row, and how do I increase the corresponding number in the second row? (For example, here, column b has the highest number, 9, so increase that number by 10%.)
I use Dyalog version 17.1.
With:
⎕←data←3 4⍴'a' 'b' 'c' 'd' 5 9 6 0 3 1 3 2
a b c d
5 9 6 0
3 1 3 2
You can extract the second row with:
2⌷data
5 9 6 0
Now grade it descending, that is, find the indices that would sort it from highest to lowest:
⍒2⌷data
2 3 1 4
The first number is the column we're looking for:
⊃⍒2⌷data
2
Now we can use this to extract the character from the first row:
data[⊂1,⊃⍒2⌷data]
b
But we only need the column index, not the actual character. The full index of the number we want to increase is:
2,⊃⍒2⌷data
2 2
Extracting the data to see that we got the right index:
data[⊂2,⊃⍒2⌷data]
9
Now we can either create a new array with the target value increased by 10%:
1.1×#(⊂2,⊃⍒2⌷data)⊢data
a b c d
5 9.9 6 0
3 1 3 2
Or change it in-place:
data[⊂2,⊃⍒2⌷data]×←1.1
data
a b c d
5 9.9 6 0
3 1 3 2
Try it online!
I have a data file that has the format of the following:
ATOM 4 N ASP A 1 105.665 49.507 41.867 1.00 71.64 N
ATOM 5 CA ASP A 1 105.992 48.589 42.982 1.00 70.20 C
ATOM 6 C ASP A 1 107.024 49.191 43.936 1.00 69.70 C
In row 1 the numbers (105.665, 49.507, and 41.867) are the columns of the coordinates (x,y,z). How do I extract the entire line with coordinates that are within a specified radius and output them in another file? The equation to correlate the coordinates to the radius is:
radius= SQRT(x^2 + y^2 +z^2)
I think you mean this:
awk -v R=124.44 '($7^2)+($8^2)+($9^2) < R^2' YourFile
Change the R=124.44 to match your radius.
Sample Output
ATOM 4 N ASP A 1 105.665 49.507 41.867 1.00 71.64 N
ATOM 5 CA ASP A 1 105.992 48.589 42.982 1.00 70.20 C
I have a text file that contains the following (a b c d etc... contains some random values):
1 a
1 b
2 c
2 d
2 e
2 f
6 g
6 h
6 i
12 j
12 k
Is there a way to separate lines with some characters depending on the content of the first string, knowing that those numbers will always be increasing, but may vary as well. The separation would be when first string is incrementing, going from 1 to 2, then 2 to 6 etc...
The output would be like this (here I would like to use ---------- as a separation):
1 a
1 b
----------
2 c
2 d
2 e
2 f
----------
6 g
6 h
6 i
----------
12 j
12 k
awk 'NR>1 && old != $1 { print "----------" } { print; old = $1 }'
If it isn't the first line and the value in old isn't the same as in $1, print the separator. Then unconditionally print the current line, and record the value of $1 in old so that we remember for next time. Repeat until done.
I have a crosstab and create custom grand total for the row level in each column dimension, by using a data element expression.
Crosstab Example:
Cat 1 Cat 2 GT
ITEM C F % VALUE C F % VALUE
A 101 0 0.9 10 112 105 93.8 10 20
B 294 8 2.7 6 69 66 95.7 10 16
C 211 7 3.3 4 212 161 75.9 6 10
------------------------------------------------------------------
GT 606 15 2.47 6 393 332 84.5 8 **14**
Explanation for GT row:
Those C and F column is summarized from the above. But the
% column is division result of F/C.
Create a data element to fill the VALUE column, which comes from range of value definition, varies for each Cat (category). For instance... in Cat 1, if the value is between 0 - 1 the value will be 10, or between 1 - 2 = 8, etc. And condition for Cat 2, between 85 - 100 = 10, and 80 - 85 = 8, etc.
The GT row (with the value of 14), is gathered by adding VALUE of Cat 1 + Cat 2.
I am able to work on point 1 and 2 above, but I can't seem to make it working for GT row. I don't know the code/expression to sum up the VALUE data element for this 2 categories. Because those VALUE field comes from one data element in design mode.
I have found the solution for my problem. I can show the result by using a report variable. I am assigning 2 report variables in % field expression, based on the category in data cube dimension (by using if statement). And then in data element expression, I am calling both of the expressions and add them.
I have files with the following format:
ATOM 8962 CA VAL W 8 8.647 81.467 25.656 1.00115.78 C
ATOM 8963 C VAL W 8 10.053 80.963 25.506 1.00114.60 C
ATOM 8964 O VAL W 8 10.636 80.422 26.442 1.00114.53 O
ATOM 8965 CB VAL W 8 7.643 80.389 25.325 1.00115.67 C
ATOM 8966 CG1 VAL W 8 6.476 80.508 26.249 1.00115.54 C
ATOM 8967 CG2 VAL W 8 7.174 80.526 23.886 1.00115.26 C
ATOM 4440 O TYR S 89 4.530 166.005 -14.543 1.00 95.76 O
ATOM 4441 CB TYR S 89 2.847 168.812 -13.864 1.00 96.31 C
ATOM 4442 CG TYR S 89 3.887 169.413 -14.756 1.00 98.43 C
ATOM 4443 CD1 TYR S 89 3.515 170.073 -15.932 1.00100.05 C
ATOM 4444 CD2 TYR S 89 5.251 169.308 -14.451 1.00100.50 C
ATOM 4445 CE1 TYR S 89 4.464 170.642 -16.779 1.00100.70 C
ATOM 4446 CE2 TYR S 89 6.219 169.868 -15.298 1.00101.40 C
ATOM 4447 CZ TYR S 89 5.811 170.535 -16.464 1.00100.46 C
ATOM 4448 OH TYR S 89 6.736 171.094 -17.321 1.00100.20 O
ATOM 4449 N LEU S 90 3.944 166.393 -12.414 1.00 94.95 N
ATOM 4450 CA LEU S 90 5.079 165.622 -11.914 1.00 94.44 C
ATOM 5151 N LEU W 8 -66.068 209.785 -11.037 1.00117.44 N
ATOM 5152 CA LEU W 8 -64.800 210.035 -10.384 1.00116.52 C
ATOM 5153 C LEU W 8 -64.177 208.641 -10.198 1.00116.71 C
ATOM 5154 O LEU W 8 -64.513 207.944 -9.241 1.00116.99 O
ATOM 5155 CB LEU W 8 -65.086 210.682 -9.033 1.00115.76 C
ATOM 5156 CG LEU W 8 -64.274 211.829 -8.478 1.00113.89 C
ATOM 5157 CD1 LEU W 8 -64.528 211.857 -7.006 1.00111.94 C
ATOM 5158 CD2 LEU W 8 -62.828 211.612 -8.739 1.00112.96 C
In principle, column 5 (W, in this case, which represents the chain ID) should be identical only in consecutive chunks. However, in files with too many chains, there are no enough letters of the alphabet to assign a single ID per chain and therefore duplicity may occur.
I would like to be able to check whether or not this is the case. In other words I would like to know if a given chain ID (A-Z, always in the 5th column) is present in non-consecutive chunks. I do not mind if it changes from W to S, I would like to know if there are two chunks sharing the same chain ID. In this case, if W or S reappear at some point. In fact, this is only a problem if they also share the first and the 6th columns, but I do not want to complicate things too much.
I do not want to print the lines, just to know the name of the file in which the issue occurs and the chain ID (in this case W), in order to solve the problem. In fact, I already know how to solve the problem, but I need to identify the problematic files to focus on those ones and not repairing already sane files.
SOLUTION (thanks to all for your help and namely to sehe):
for pdb in $(ls *.pdb) ; do
hit=$(awk -v pdb="$pdb" '{ if ( $1 == "ATOM" ) { print $0 } }' $pdb | cut -c22-23 | uniq | sort | uniq -dc)
[ "$hit" ] && echo $pdb = $hit
done
For this particular sample:
cut -c22-23 t | uniq | sort | uniq -dc
Will output
2 W
(the 22nd column contains 2 runs of the letter 'W')
untested
awk '
seen[$5] && $5 != current {
print "found non-consecutive chain on line " NR
exit
}
{ current = $5; seen[$5] = 1 }
' filename
Here you go, this awk script is tested and takes into account not just 'W':
{
if (ln[$5] && ln[$5] + 1 != NR) {
print "dup " $5 " at line " NR;
}
ln[$5] = NR;
}