I would like to insert columns no. 1 and 2 from file no. 2 into file no. 1 after every second column and till the last column.
File1.txt (tab-separated, column range from 1-2400 and cell range from 1-4500)
ID IMPACT ID IMPACT ID IMPACT
51 0.288 128 0.4557 156 0.85
625 0.858 15 -0.589 51 0.96
8 0.845 7 0.5891
File2.txt (consist of only two-tab separated column with 19000 raws)
ID IMPACT
18 -1
165 -1
41 -1
11 -1
Output file
ID IMPACT ID IMPACT ID IMPACT ID IMPACT ID IMPACT ID IMPACT
51 0.288 18 -1 128 0.4557 18 -1 156 0.85 18 -1
625 0.858 165 -1 15 -0.589 165 -1 51 0.96 165 -1
8 0.845 41 -1 7 0.5891 41 -1 41 -1
11 -1 11 -1 11 -1
I tried the below commands but it's not working
paste <(cut -f 1,2 File1.txt) <(cut -f 1,2 File2.txt) <(cut -f 3,4 File1.txt) <(cut -f 1,2 File2.txt)......... > File3
Prob: It starts sifting the File2.txt column value into different columns after the highest cell of File1.txt
paste File1.txt File2.txt > File3.txt
awk '{print $1 "\t" $2 "\t" $3 "\t" $4 "\t" $5 "\t" $6 "\t" $3 "\t" $4....}' File3.txt > File4.txt
This do the job, however it mixup the value of File1.txt from one column to another column.
I tried everything but failed to succeed.
Any help would be appreciated, however, bash or pandas would be better. Thanks in advance.
$ awk '
BEGIN {
FS=OFS="\t" # tab-separated data
}
NR==FNR { # hash fields of file2
a[FNR]=$1 # index with record numbers FNR
b[FNR]=$2
next
}
{ # print file1 records with file2 fields
print $1,$2,a[FNR],b[FNR],$3,$4,a[FNR],b[FNR],$5,$6,a[FNR],b[FNR]
}
END { # in the end
for(i=(FNR+1);(i in a);i++) # deal with extra records of file2
print "","",a[i],b[i],"","",a[i],b[i],"","",a[i],b[i]
}' file2 file1
Output:
ID IMPACT ID IMPACT ID IMPACT ID IMPACT ID IMPACT ID IMPACT
51 0.288 18 -1 128 0.4557 18 -1 156 0.85 18 -1
625 0.858 165 -1 15 -0.589 165 -1 51 0.96 165 -1
8 0.845 41 -1 7 0.5891 41 -1 41 -1
11 -1 11 -1 11 -1
Related
I tried to use awk to select all rows with a value greater than 98 in the third column. In the output, only lines between 98 - 98.99... were selected and lines with a value more than 98.99 not.
I would like to extract all lines with a value greater than 98 including 99, 100 and so on.
Here my code and my input format:
for i in *input.file; do awk '$3>98' $i >{i/input./output.}; done
A chr11 98.80 83 1 0 2 84
B chr7 95.45 22 1 0 40 61
C chr7 88.89 27 0 1 46 72
D chr6 100.00 20 0 0 1 20
Expected Output
A chr11 98.80 83 1 0 2 84
D chr6 100.00 20 0 0 1 20
Okay, if you have a series of files, *input.file and you want to select those lines where $3 > 98 and then write the values to the same prefix, but with output.file as the rest of the filename, you can use:
awk '$3 > 98 {
match (FILENAME,/input.file$/)
print $0 > substr(FILENAME,1,RSTART-1) "output.file"
}' *input.file
Which uses match to find the index where input.file begins and then uses substr to get the part of the filename before that and appends "output.file" to the substring for the final output filename.
match() sets the RSTART value to the index where input.file begins in the current filename which is then used by substr truncate the current filename at that index. See GNU awk String Functions for complete details.
For exmaple, if you had input files:
$ ls -1 *input.file
v1input.file
v2input.file
Both with your example content:
$ cat v1input.file
A chr11 98.80 83 1 0 2 84
B chr7 95.45 22 1 0 40 61
C chr7 88.89 27 0 1 46 72
D chr6 100.00 20 0 0 1 20
Running the awk command above would results in two output files:
$ ls -1 *output.file
v1output.file
v2output.file
Containing the records where the third-field was greater than 98:
$ cat v1output.file
A chr11 98.80 83 1 0 2 84
D chr6 100.00 20 0 0 1 20
I am trying to sum certain numbers in colum 2, it works with my code. But I want to count also how many times the same value in colum 2 is repeated and print in the last column.
file1
36 2605 1 2
36 2605 1 2
36 2603 1 2
36 2605 1 2
36 2605 1 2
36 2605 1 2
36 2606 1 2
Output Desired
2603 36 1 2 1
2605 180 5 10 5
2606 36 1 2 1
I tried
awk '{a[$2]+=$1}{b[$2]+=$3}{c[$2]+=$4;count[$2]+=$2}END{for(i in a)print i,a[i],b[i],c[i],count[i]}' file1
Thanks in advance
Renamed the vars and added pretty print:
awk '
{
sum1[$2]+=$1
sum3[$2]+=$3
sum4[$2]+=$4
count[$2]++
len2=((l=length($2))>len2?l:len2)
len1=((l=length(sum1[$2]))>len1?l:len1)
len3=((l=length(sum3[$2]))>len3?l:len3)
len4=((l=length(sum4[$2]))>len4?l:len4)
len5=((l=length(sum5[$2]))>len5?l:len5)
}
END {
for(i in count) {
printf "%*d %*d %*d %*d %*d\n",
len2,i,len1,sum1[i],len3,sum3[i],len4,sum4[i],len5,count[i]
}
}' file
Output:
2603 36 1 2 1
2605 180 5 10 5
2606 36 1 2 1
Space chars are relatively inexpensive these days, you should really consider getting some for your code, especially if you want other people to read it to help you debug it! Here's the code you posted:
awk '{a[$2]+=$1}{b[$2]+=$3}{c[$2]+=$4;count[$2]+=$2}END{for(i in a)print i,a[i],b[i],c[i],count[i]}' file1
and here it is after having been run through a code beautifier (I used gawk -o):
{
a[$2] += $1
}
{
b[$2] += $3
}
{
c[$2] += $4
count[$2] += $2
}
END {
for (i in a) {
print i, a[i], b[i], c[i], count[i]
}
}
See how just by adding some white space it's now vastly easier to understand and so the bug in how count[$2] is being populated is glaringly obvious? Some meaningful variable names are always extremely useful too and I hear alphanumeric chars are on special right now!
FWIW here's how I'd do this:
$ cat tst.awk
BEGIN { keyFldNr = 2 }
{
numOutFlds = 0
for (i=1; i<=NF; i++) {
if (i != keyFldNr) {
sum[$keyFldNr,++numOutFlds] += $i
}
}
cnt[$keyFldNr]++
}
END {
for (key in cnt) {
printf "%s%s", key, OFS
for (i=1; i<=numOutFlds; i++) {
printf "%s%s", sum[key,i], OFS
}
print cnt[key]
}
}
$ awk -f tst.awk file
2603 36 1 2 1
2605 180 5 10 5
2606 36 1 2 1
$ awk -f tst.awk file | column -t
2603 36 1 2 1
2605 180 5 10 5
2606 36 1 2 1
Notice that it'll work as-is no matter how many fields you have on each line and if you need to use a different field for the key that you count and sum on then you just change the value of keyFldNr in the BEGIN section from 2 to whatever you want it to be.
A non-awk approach, using the very useful GNU datamash, which is designed for tasks like this one:
$ datamash -Ws groupby 2 sum 1,3,4 count 2 < input.txt
2603 36 1 2 1
2605 180 5 10 5
2606 36 1 2 1
Read as: For each group of rows with the same value in column 2, display that value, the sums of columns 1, 3 and 4, and the number of rows in the group.
You've almost nailed it, you're not increasing count[$2] properly.
$ awk '{a[$2]+=$1;b[$2]+=$3;c[$2]+=$4;count[$2]++}
END{for(i in a) print i,a[i],b[i],c[i],count[i]}' file
2603 36 1 2 1
2605 180 5 10 5
2606 36 1 2 1
no need external program, faster ~21ms, tried on pure gnu awk
awk '{if($0~/^[A-Za-z0-9]/)a[NR]=$2" "$1" "$3" "$4}END{asort(a);$0="";for(;i++<NR;){split(a[i],b);if($1==""||b[1]==$1){$2+=b[2];$3+=b[3];$4+=b[4];$5++} else {print;$2=b[2];$3=b[3];$4=b[4];$5=1} $1=b[1]} print}' file1
I'm trying to match two files,file1.txt(50,000 lines), file2.txt(55,000 lines). I want to campare file2 to file 1 extract the values of column 2 and 3 and leave the mismatches as such. Output file must contain all the ids from file2 i.e., it should have 55000 lines. Note: All the ids in file 1 are not present in file2. i.e the actual matches could be less than 50,000.
file1.txt
ab1 12 345
ab2 9 456
gh67 6 987
file2.txt
ab2 0 0
ab1 0 345
nh7 0 0
gh67 6 987
Output
ab2 9 456
ab1 12 345
nh7 0 0
gh67 6 987
This is what i tried but it only print the matches (so instead of 55,000 lines i have 49,000 lines in my output file)
awk "NR==FNR {f[$1]=$0;next}$1 in f{print f[$1],$0}" file1.txt file2.txt >output.txt
This awk script will work
NR == FNR {
a[$1] = $0
next
}
$1 in a {
split(a[$1], b)
print $1, (b[2] == $2 ? $2 : b[2]), (b[3] == $3 ? $3 : b[3])
}
!($1 in a)
If you save this as a.awk and run
awk -f a.awk foo.txt foo1.txt
This will output
ab2 9 456
ab1 12 345
nh7 0 0
gh67 6 987
I have a file named file.txt as shown below
12 2
15 7
134 8
154 12
155 16
167 6
175 45
45 65
812 54
I have another five files named A.txt, B.txt, C.txt, D.txt, E.txt. The contents of these files are shown below.
A.txt
45
134
B.txt
15
812
155
C.txt
12
154
D.txt
175
E.txt
167
I need to check, which file contains the values of first column of file.txt exists and print the name of the file as third column.
Output:-
12 2 C
15 7 B
134 8 A
154 12 C
155 16 B
167 6 E
175 45 D
45 65 A
812 54 B
This should work:
One-liner:
awk 'FILENAME != "file.txt"{ a[$1]=FILENAME; next } $1 in a { $3=a[$1]; sub(/\..*/,"",$3) }1' {A..E}.txt file.txt
Formatted with comments:
awk '
#Check if the filename is not of the main file
FILENAME != "file.txt" {
#Create a hash. Store column 1 values of look up files as key and assign filename as values
a[$1]=FILENAME
#Skip the rest of the action
next
}
#Check the first column of main file is a key in the hash
$1 in a {
#If the key exists, assign the value of the key (which is filename) as Column 3 of main file
$3=a[$1]
#Using sub function, strip the extension of the file name as desired in your output
sub(/\..*/,"",$3)
#1 is a non-zero value forcing awk to print. {A..E} is brace expansion of your files.
}1' {A..E}.txt file.txt
Note: The main file needs to be passed at the end.
Test:
[jaypal:~/Temp] awk 'FILENAME != "file.txt"{ a[$1]=FILENAME; next } $1 in a { $3=a[$1]; sub(/\..*/,"",$3) ; printf "%-5s%-5s%-5s\n",$1,$2,$3}' {A..E}.txt file.txt
12 2 C
15 7 B
134 8 A
154 12 C
155 16 B
167 6 E
175 45 D
45 65 A
812 54 B
#! /usr/bin/awk -f
FILENAME == "file.txt" {
a[FNR] = $0;
c=FNR;
}
FILENAME != "file.txt" {
split(FILENAME, name, ".");
k[$1] = name[1];
}
END {
for (line = 1; line <= c; line++) {
split(a[line], seg, FS);
print a[line], k[seg[1]];
}
}
# $ awk -f script.awk *.txt
This solution does not preserve the order
join <(sort file.txt) \
<(awk '
FNR==1 {filename = substr(FILENAME, 1, length(FILENAME)-4)}
{print $1, filename}
' [ABCDE].txt |
sort) |
column -t
12 2 C
134 8 A
15 7 B
154 12 C
155 16 B
167 6 E
175 45 D
45 65 A
812 54 B
I have file1 as a result of a first operation, it has the following structure
201 12 0.298231 8.8942
206 13 -0.079795 0.6367
101 34 0.86348 0.7456
301 15 0.215355 4.6378
303 16 0.244734 5.9895
and file2 as a result of a different operation and has the same type of structure.
File 2 sample
204 60 -0.246038 6.0535
304 83 -0.246209 6.0619
101 34 -0.456629 6.0826
211 36 -0.247003 6.1011
305 83 -0.247134 6.1075
206 46 -0.247485 6.1249
210 39 -0.248066 6.1537
107 41 -0.248201 6.1603
102 20 -0.248542 6.1773
I would like to select fields 1 and 2 that have a field 3 value higher than a threshold in file1 (0.8) , then for these selected values of field 1 and 2, select the values that have a field 3 value higher than another threshold in file 2 (abs(x)=0.4).
Note that although files 1 and 2 have the same structure fields 1 and 2 values are not the same (not the same number of lines etc..)
Can you do this with awk?
desired output
101 34
If you combine awk with unix commands you can do the following
sort file1.txt > sorted1.txt
sort file2.txt > sorted2.txt
Sorting will allow you to use JOIN on the first line (which I assume is unique). Now field 3 of file1 is $3 and file2 is $6. Using awk you can write the following.:
join sorted1.txt sorted2.txt | awk 'function abs(value){return (value<0?-value:value);}{print $1"\t"$2} $3 >=0.8 && abs($6) >=0.4'
In essence, in the awk you first write a function to deal with absolute values, then you simply ask it to print line 1 and 2 selecting for the criteria you detailed at $3 and $6 (formely field 3 of file1 and file2 respectively)
Hope this helps...