I'm trying to make this loop work
for i in 5 10 15; do awk -v var=${i} '$2>var' file.txt > par${i}.pos; done
Where file.txt is a tab delim like in
A 2
B 4
EE 5
F2 7
FF 12
C 5
D 13
GAG 15
so that I can collect lines of file.txt that have 2nd col > 5 in par5.pos and so on, but it doesn't work.
As in par5.pos
F2 7
FF 12
D 13
GAG 15
or par10.pos
FF 12
D 13
GAG 15
This might work for you (GNU parallel and awk):
parallel awk \''$2>{}'\' file '>' pos{}.pos ::: 5 10 15
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 am trying to turn a 1xA table into a BxC table. Let's say A is 15, B is 3 and C is 5, hence after each 5 entries I want it to start a new row in the same table.
I have a rather tedious way that appears to get close be it misses some values after each 5. I think the issue is with RS, as a new line forgets the "space" needed by RS, but I tried changing this to something else in file.sum and still no luck. Perhaps there is a better way to do it, but feel this should work.
awk -v RS=" " '{getline a1; getline a2; getline a3; getline a4; getline a5; print a1,a2,a3,a4,a5}' OFS='\t' file.sum
file.sum (my 1xA):
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
Expected results (my BxC):
1 2 3 4 5
6 7 8 9 10
11 12 13 14 15
Actual results:
1 2 3 4 5
7 8 9 10 11
13 14 15 10 11
This should be one of the simplest solution:
xargs -n5 <file
1 2 3 4 5
6 7 8 9 10
11 12 13 14 15
To follow up on your awk. I do not like the getline so I always try to avoid it. Also loop slows down awk some.
But using RS=" " you can do like this:
awk -v RS=" " '{$1=$1} {printf NR%5==0?"%s\n":"%s ",$0}' file
1 2 3 4 5
6 7 8 9 10
11 12 13 14 15
You can remove the {$1=$1}, but will then get a blank line at the end.
The NR%5==0 test if record is every 5th and insert newline when needed.
A tab version:
awk -v RS=" " '{$1=$1} {printf NR%5==0?"%s\n":"%s\t",$0}' file
1 2 3 4 5
6 7 8 9 10
11 12 13 14 15
I have a file first.txt that looks like this :
45
56
74
62
I want to append this file to second.tsv that looks like this(there are 17 columns) :
2 a ...
3 b ...
5 c ...
6 d ...
The desired output is :
2 45 a ...
3 56 b ...
5 74 c ...
6 62 d ...
How can I append to the second column?
I've tried
awk -F, '{getline f1 <"first.txt" ;print $1,f1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12,$13,$14,$15,$16,$17}' second.tsv
but did not work. This added the columns of first.txt to the last column of second.tsv, and it was not tab separated.
Thank you.
Your code works if you remove the -F, bit. This tells awk that the file is comma-separated, which it is not.
Another option would be to go for a piped version with paste, e.g.:
paste first.tsv second.tsv | awk '{ t=$2; $2=$1; $1=t } 1' OFS='\t'
Output:
2 45 a ...
3 56 b ...
5 74 c ...
6 62 d ...
$ awk 'NR==FNR{a[FNR]=$0;next} {$1=$1 OFS a[FNR]} 1' file1 file2
2 45 a ...
3 56 b ...
5 74 c ...
6 62 d ...
If your files are tab-separated add BEGIN{FS=OFS="\t"} at the front.
I have large file with 1000 columns. I want to rearrange so that last column should be the 3rd column. FOr this i have used,
cut -f1-2,1000,3- file > out.txt
But this does not change the order.
Could anyone help using cut or awk?
Also, I want to rearrange columns 10 and 11 as shown below:
Example:
1 10 11 2 3 4 5 6 7 8 9 12 13 14 15 16 17 18 19 20
try this awk one-liner:
awk '{$3=$NF OFS $3;$NF=""}7' file
this is moving the last col to the 3rd col. if you have 1000, then it does it with 1000th col.
EDIT
if the file is tab-delimited, you could try:
awk -F'\t' -v OFS="\t" '{$3=$NF OFS $3;$NF=""}7' file
EDIT2
add an example:
kent$ seq 20|paste -s -d'\t'
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
kent$ seq 20|paste -s -d'\t'|awk -F'\t' -v OFS="\t" '{$3=$NF OFS $3;$NF=""}7'
1 2 20 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19
EDIT3
You didn't give any input example. so assume you don't have empty columns in original file. (no continuous multi-tabs):
kent$ seq 20|paste -s -d'\t'|awk -F'\t' -v OFS="\t" '{$3=$10 FS $11 FS $3;$10=$11="";gsub(/\t+/,"\t")}7'
1 2 10 11 3 4 5 6 7 8 9 12 13 14 15 16 17 18 19 20
After all we could print those fields in a loop.
I THINK what you want is:
awk 'BEGIN{FS=OFS="\t"} {$3=$NF OFS $3; sub(OFS "[^" OFS "]*$","")}1' file
This might also work for you depending on your awk version:
awk 'BEGIN{FS=OFS="\t"} {$3=$NF OFS $3; NF--}1' file
Without the part after the semi-colon you'll have trailing tabs in your output.
Since many people are searching for this and even the best awk solution is not really pretty and easy to use I wanted to post my solution (mycut) written in Python:
#!/usr/bin/env python3
import sys
from signal import signal, SIGPIPE, SIG_DFL
signal(SIGPIPE,SIG_DFL)
#example usage: cat file | mycut 3 2 1
columns = [int(x) for x in sys.argv[1:]]
delimiter = "\t"
for line in sys.stdin:
parts = line.split(delimiter)
print("\t".join([parts[col] for col in columns]))
I think about adding the other features of cut like changing the delimiter and a feature to use a * to print the remaning columns. But then it will get an own page.
A shell wrapper function for awk' that uses simpler syntax:
# Usage: rearrange int_n [int_o int_p ... ] < file
rearrange ()
{
unset n;
n="{ print ";
while [ "$1" ]; do
n="$n\$$1\" \" ";
shift;
done;
n="$n }";
awk "$n" | grep '\w'
}
Examples...
echo foo bar baz | rearrange 2 3 1
bar baz foo
Using bash brace expansion, rearrange first and last 5 items in descending order:
echo {1..1000}a | tr '\n' ' ' | rearrange {1000..995} {5..1}
1000a 999a 998a 997a 996a 995a 5a 4a 3a 2a 1a
Sorted 3-letter shells in /bin:
ls -lLSr /bin/?sh | rearrange 5 9
150792 /bin/csh
154072 /bin/ash
771552 /bin/zsh
1554072 /bin/ksh
zcat *.gz | awk '{print $1}' |sort| uniq -c | sed 's/^[ ]\+//g' | cut -d' ' -f1 | sort | uniq -c | sort -k1n
I get the following output:
3 648
3 655
3 671
3 673
3 683
3 717
4 18
4 29
4 31
4 34
4 652
5 12
6 24
6 33
7 13
12 10
13 9
14 8
33 7
73 6
166 5
383 4
1178 3
3945 2
26692 1
I don't want repetitions in my 1st column. Example: if my first column is 3 , i should add all the values in the second column that are associated with 3. Thank you
Solution using arrays in awk
{
a[$1]=a[$1]+$2
}
END {
for (i in a)
printf("%d\t%d\n", i, a[i])
}
Pipe the output through sort -n once more to have it in ascending order
$ awk -f num.awk numbers | sort -n
3 4047
4 764
5 12
6 57
7 13
12 10
13 9
14 8
33 7
73 6
166 5
383 4
1178 3
3945 2
26692 1
awk 'NF == 1 {c=$1; print $0} NF>1 {if (c==$1) {print "\t" $2} else {c=$1; print $0}}'
can do it, but please note, that the indentation can be incorrect, as I had used a simple tab \t above.
HTH