From a tab delimited file. I'm trying to extract all rows based on a unique value from column 4 and then save it as a CSV. However, I would like to extract all the distinct values in column 4 and save them as CSV in one go.
I was able to extract one value using this command:
awk -F $'\t' '$4 == "\"C333\"" {print}' dataFile > C333.csv
Let's consider this test file:
$ cat in.csv
a b c d
aa bb cc d
1 2 3 4
12 23 34 4
A B C d
Now, let's write each row to a tab-separated output file that is named after the fourth column:
$ awk -F'\t' '{f=$4".csv"; print>>f; close(f)}' OFS='\t' in.csv
$ cat d.csv
a b c d
aa bb cc d
A B C d
$ cat 4.csv
1 2 3 4
12 23 34 4
Related
I have an AWK program that does a join of two files, file1 and file2. The files are joined based on a set of columns. I placed the AWK program into a bash script that I named join.sh. See below. Here is an example of how the script is executed:
./join.sh '1,2,3,4' '2,3,4,5' file1 file2
That says this: Do a join of file1 and file2, using columns (fields) 1,2,3,4 of file1 and columns (fields) 2,3,4,5 of file2.
That works great.
Now what I would like to do is to filter file2 and pipe the results to the join tool:
./fetch.sh ident file2 | ./join.sh '1,2,3,4' '2,3,4,5' file1
fetch.sh is a bash script containing an AWK program that fetches the rows in file2 with primary key ident and outputs to stdout the rows that were fetched.
Unfortunately, that pipeline is not working. I get no results.
Recap: I want the join program to be able to read the second file either from a file that I specify on the command line or from data received via a pipe. How to do that?
Here is my bash script, named join.sh
#!/bin/bash
awk -v f1cols=$1 -v f2cols=$2 '
BEGIN { FS=OFS="\t"
m=split(f1cols,f1,",")
n=split(f2cols,f2,",")
}
{ sub(/\r$/, "") }
NR == 1 { b[0] = $0 }
(NR == FNR) && (NR > 1) { idx2=$(f2[1])
for (i=2;i<=n;i++)
idx2=idx2 $(f2[i])
a[idx2] = $0
next
}
(NR != FNR) && (FNR == 1) { print $0, b[0] }
FNR > 1 { idx1=$(f1[1])
for (i=2;i<=m;i++)
idx1=idx1 $(f1[i])
for (idx1 in a)
print $0, a[idx1]
}' $3 $4
I'm not sure if this is 'correct' as you haven't provided any example input and expected output, but does using - to signify stdin work for your use-case? E.g.
cat file1
1 2 3 4
AA BB CC DD
AA EE FF GG
cat file2
1 2 3 4
AA ZZ YY XX
AA 11 22 33
./join.sh '1' '1' file1 file2
1 2 3 4 1 2 3 4
AA ZZ YY XX AA BB CC DD
AA ZZ YY XX AA EE FF GG
AA 11 22 33 AA BB CC DD
AA 11 22 33 AA EE FF GG
cat file2 | ./join.sh '1' '1' file1 -
1 2 3 4 1 2 3 4
AA ZZ YY XX AA BB CC DD
AA ZZ YY XX AA EE FF GG
AA 11 22 33 AA BB CC DD
AA 11 22 33 AA EE FF GG
be able to read(...)from data received via a pipe
GNU AWK does support Using getline from a Pipe consider following simple example
awk 'BEGIN{cmd="seq 7";while((cmd | getline) > 0){print $1*7};close(cmd)}' emptyfile
gives output
7
14
21
28
35
42
49
Explanation: I process output of seq 7 command (numbers from 1 to 7 inclusive, each on separate line), body of while is executed for each line of seq 7 output, fields are set like for normal processing.
I have millions of records in my file, what i need to do is print columns 1396 to 1400 for specific number of rows, and if i can get this in excel or notepad.
Tried with this command
awk {print $1396,$1397,$1398,$1399,$1400}' file_name
But this is running for each row.
You need a condition to specify which rows to apply the action to:
awk '<<condition goes here>> {print $1396,$1397,$1398,$1399,$1400}' file_name
For example, to do this only for rows 50 to 100:
awk 'NR >= 50 && NR <= 100 {print $1396,$1397,$1398,$1399,$1400}' file_name
(Depending on what you want to do, you can also have much more complicated selection patterns than this.)
Here's a simpler example for testing:
awk 'NR >= 3 && NR <= 5 {print $2, $3}'
If I run this on an input file containing
1 2 3 4
2 3 4 5
3 a b 6
4 c d 7
5 e f 8
6 7 8 9
I get the output
a b
c d
e f
Here is my Input file
Identifier Relation
A 1
A 2
A 3
B 2
B 3
C 1
C 2
C 3
I want to join this file to itself based on the "Relation" field.
Sample Output file
A 1 C 1
A 2 B 2
A 2 C 2
B 2 C 2
A 3 B 3
A 3 C 3
B 3 C 3
I used the following awk script:
awk 'NR==FNR {a[NR]=$0; next} { for (k in a) if (a[k]~$2) print a[k],$0}' input input > output
However, I had to do another awk step to delete lines which did a join with itself i.e, A 1 A 1 ; B 2 B 2 etc.
The second issue with this file is it prints both directions of the join, thus
A 1 C 1 is printed along with C 1 A 1 on another line.
Both these lines display the same relation and I would NOT like to include this.I want to see just one or the other i.e, "A 1 C 1" or "C 1 A 1" not both.
Any suggestions/directions are highly appreciated.
alternative solution using awk with join and sort support
$ join -j 2 <(sort -k2 -k1,1 file){,}
| awk '$2!=$3 && !($3 FS $2 in a){a[$2 FS $3]; print$2,$1,$3,$1}'
A 1 C 1
A 2 B 2
A 2 C 2
B 2 C 2
A 3 B 3
A 3 C 3
B 3 C 3
create the cross product, eliminate the diagonal and one of the symmetrical pairs.
Here is an awk-only solution:
awk 'NR>1{ar[$2]=(ar[$2]$1);}\
END{ for(key in ar){\
for(i=1; i<length(ar[key]); i++) {\
for(j=i+1; j<length(ar[key])+1; j++) {\
print substr(ar[key],i,1), key, substr(ar[key],j,1), key;\
}\
}\
}}' infile
Each number in the second column of the input serves as a key of an awk-array. The value of the corresponding array-element is a sequence of first-column letters (e.g., array[1]=ABC).
Then, we built all two-letter combinations for each sequence (e.g., "ABC" gives "AB", "AC" and "BC")
Output:
A 1 C 1
A 2 B 2
A 2 C 2
B 2 C 2
A 3 B 3
A 3 C 3
B 3 C 3
Note:
If a number occurs only once, no output is generated for this number.
The order of output depends on the order of input. (No sorting of letters!!). That is if the second input line was C 1, then array[1]="CAB" and the first output line would be C 1 A 1
First line of input is ignored due to NR>1
There is surely a solution with awk only, but I'm going to propose a solution using awk and sort because I think it's quite simple and does not require storing the entire file content in awk variables. The idea is as follows:
rewrite the input file so that the "relation" field is first (A 1 -> 1 A)
use sort -n to put together all lines with same "relation"
use awk to combine consecutive lines having the same "relation"
That would translate to something like:
awk '{print $2 " " $1}' input | sort -n |
awk '{if ($1==lastsel)printf " "; else if(lastsel) printf "\n"; lastsel=$1; printf "%s %s", $2, $1;}END{if(lastsel)printf"\n"}'
A 1 C 1
A 2 B 2 C 2
A 3 B 3 C 3
EDIT: If you want only one i-j relation per line:
awk '{print $2 " " $1}' input | sort -n |
awk '$1!=rel{rel=$1;item=$2;next;} {printf "%s %s %s %s\n", item, rel, $2, $1;}'
A 1 C 1
A 2 B 2
A 2 C 2
A 3 B 3
A 3 C 3
Note the following limitations with this solution:
In case a given n has only one entry, nothing will be output (no output such as D 1)
All relations always have the lexicographically first item in the first column (e.g. A 1 C 1 but never B 1 C 1)
I have a 4 column data that looks something like the following:
a 1 g 1,2,3,4,5,6,7
b 2 g 3,5,3,2,6,4,3,2
c 3 g 5,2,6,3,4
d 4 g 1,5,3,6,4,7
I am trying to delete first two numbers and the last two numbers on entire fourth column so the output looks like the following
a 1 g 3,4,5
b 2 g 3,2,6,4
c 3 g 6
d 4 g 3,6
Can someone give me a help? I would appreciate it.
You can use this:
$ awk '{n=split($4, a, ","); for (i=3; i<=n-2; i++) t=t""a[i](i==n-2?"":","); print $1, $2, $3, t; t=""}' file
a 1 g 3,4,5
b 2 g 3,2,6,4
c 3 g 6
d 4 g 3,6
Explanation
n=split($4, a, ",") slices the 4th field in pieces, based on comma as delimiter. As split() returns the number of pieces we got, we store it in n to work with it later on.
for (i=3; i<=n-2; i++) t=t""a[i](i==n-2?"":",") stores in t the last field, looping through all the slices.
print $1, $2, $3, t; t="" prints the new output and blanks the variable t.
This will work for your posted sample input:
$ awk '{gsub(/^([^,]+,){2}|(,[^,]+){2}$/,"",$NF)}1' file
a 1 g 3,4,5
b 2 g 3,2,6,4
c 3 g 6
d 4 g 3,6
If you have cases where there's less than 4 commas in your 4th field then update your question to show how those should be handled.
This uses bash array manipulation. It may be a little ... gnarly:
while read -a fields; do # read the fields for each line
IFS=, read -a values <<< "${fields[3]}" # split the last field on comma
new=("${values[#]:2:${#values[#]}-4}") # drop the first 2 and last fields
fields[3]=$(IFS=,; echo "${new[*]}") # join the new list on comma
printf "%s\t" "${fields[#]}"; echo # print the new line
done <<END
a 1 g 1,2,3,4,5,6,7
b 2 g 3,5,3,2,6,4,3,2
c 3 g 5,2,6,3,4
d 4 g 1,5,3,6,4,7
END
a 1 g 3,4,5
b 2 g 3,2,6,4
c 3 g 6
d 4 g 3,6
I wanted to merge two files into a single one line by line using the first three columns as a key. Example:
file1.txt
a b c 1 4 7
x y z 2 5 8
p q r 3 6 9
file2.txt
p q r 11
a b c 12
x y z 13
My desired output for the above two files is:
a b c 1 4 7 12
x y z 2 5 8 13
p q r 3 6 9 11
The number of columns in each file is not fixed, it can vary from line to line. Also, I got more than 27K lines in each file.
They are not ordered. They only thing is that the first three fields are the same for both files.
You could also use join, it requires sorted input and that the first 3 fields are merged. The example below sorts each file and lets sed merge and separate the fields:
join <(sort file1.txt | sed 's/ /-/; s/ /-/') \
<(sort file2.txt | sed 's/ /-/; s/ /-/') |
sed 's/-/ /; s/-/ /'
Output:
a b c 1 4 7 12
p q r 3 6 9 11
x y z 2 5 8 13
Join on the first three fields where the number of fields are variable (four or more):
{
# get the forth field until the last
for (i=4;i<=NF;i++)
f=f$i" "
# concat fields
arr[$1OFS$2OFS$3]=arr[$1OFS$2OFS$3]f;
# reset field string
f=""
}
END {
for (key in arr)
print key, arr[key]
}
Run like:
$ awk -f script.awk file1 file2
a b c 1 4 7 12
p q r 3 6 9 11
x y z 2 5 8 13
try this:
awk 'NR==FNR{a[$1$2$3]=$4;next}$1$2$3 in a{print $0, a[$1$2$3]}' file2 file1
If the columns have varying lengths, you could try something like this using SUBSEP:
awk 'NR==FNR{A[$1,$2,$3]=$4; next}($1,$2,$3) in A{print $0, A[$1,$2,$3]}' file2 file1
For varying columns in file1 and sorted output, try:
awk '{$1=$1; i=$1 FS $2 FS $3 FS; sub(i,x)} NR==FNR{A[i]=$0; next}i in A{print i $0, A[i]}' file2 file1 | sort