I am trying to sort with awk a large csv file by id's in the first column on OSX.
I started with:
awk -F, 'NR>1 {print > ($1 ".sync")}' file.csv
However, the process stopped at ID s_17 with the error:
awk: s_18.sync makes too many open files input record number 37674601,
file file.csv source line number 1
I tried modifying with this close() statement but it then only writes the first file
awk -F, 'NR>1 {print > ($1 ".sync");close($1 ".sync"}' file.csv
Can anyone provide insight on how to close the files after each one, properly, so that the number of open files stays manageable but they all get written?
Because you close the file you need to use the append >> operator so you don't clobber the output files:
$ awk -F, 'NR>1{f=$1".sync";print >> f;close(f)}' file.csv
Check out the manual for the official word on redirection with awk.
Don't sort with awk. AWK is great to format data before sorting. Pipe the output into sort(1) and let it sort the data. That's what sort does, and it does a great job.
Also - which type of sort do you need? Dictionary? Numeric? Do you need to ignore spaces?
example:
sort -t, -n <file
Related
I have a directory with multiple csv text files, each with a single line in the format:
field1,field2,field3,560
I need to output the sum of the fourth field across all files in a directory (can be hundreds or thousands of files). So for an example of:
file1.txt
field1,field2,field3,560
file2.txt
field1,field2,field3,415
file3.txt
field1,field2,field3,672
The output would simply be:
1647
I've been trying a few different things, with the most promising being an awk command that I found here in response to another user's question. It doesn't quite do what I need it to do, and I am an awk newb so I'm unsure how to modify it to work for my purpose:
awk -F"," 'NR==FNR{a[NR]=$4;next}{print $4+a[FNR]:' file1.txt file2.txt
This correctly outputs 975.
However if I try pass it a 3rd file, rather than add field 4 from all 3 files, it adds file1 to file2, then file1 to file3:
awk -F"," 'NR==FNR{a[NR]=$4;next}{print $4+a[FNR]:' file1.txt file2.txt file3.txt
975
1232
Can anyone show me how I can modify this awk statement to accept more than two files or, ideally because there are thousands of files to sum up, an * to output the sum of the fourth field of all files in the directory?
Thank you for your time and assistance.
A couple issues with the current code:
NR==FNR is used to indicate special processing for the 1st file; in this case there is no processing that is 'special' for just the 1st file (ie, all files are to be processed the same)
an array (eg, a[NR]) is used to maintain a set of values; in this case you only have one global value to maintain so there is no need for an array
Since you're only looking for one global sum, a bit more simpler code should suffice:
$ awk -F',' '{sum+=$4} END {print sum+0}' file{1..3}.txt
1647
NOTES:
in the (unlikely?) case all files are empty, sum will be undefined so print sum will display a blank link; sum+0 insures we print 0 if sum remains undefined (ie, all files are empty)
for a variable number of files file{1..3}.txt can be replaced with whatever pattern will match on the desired set of files, eg, file*.txt, *.txt, etc
Here we go (no need to test NR==FNR in a concatenation):
$ cat file{1,2,3}.txt | awk -F, '{count+=$4}END{print count}'
1647
Or same-same 🇹🇠(without wasting some pipe(s)):
$ awk -F, '{count+=$4}END{print count}' file{1,2,3}.txt
1647
$ perl -MList::Util=sum0 -F, -lane'push #a,$F[3];END{print sum0 #a}' file{1..3}.txt
1647
$ perl -F, -lane'push #a,$F[3];END{foreach(#a){ $sum +=$_ };print "$sum"}' file{1..3}.txt
1647
$ cut -d, -f4 file{1..3}.txt | paste -sd+ - | bc
1647
cat file1.txt | awk -F '{print $1 "|~|" $2 "|~|" $3}' > file2.txt
I am using above command to filter first three columns from file1 and put into file.
But only getting the column names and not the column data.
How to do that?
|~| - is the delimiter.
file1.txt has values as :
a|~|b|~|c|~|d|~|e
1|~|2|~|3|~|4|~|5
11|~|22|~|33|~|44|~|55
111|~|222|~|333|~|444|~|555
my expedted output is :
a|~|b|~|c
1|~|2|~|3
11|~|22|~|33
111|~|222|~|333
With your shown samples, please try following awk code. You need to set field separator to |~| and remove starting space from lines, then print the lines.
awk -F'\\|~\\|' -v OFS='|~|' '{sub(/^[[:blank:]]+/,"");print $1,$2,$3}' Input_file
In case you want to keep spaces(which was in initial post before edit) then try following:
awk -F'\\|~\\|' -v OFS='|~|' '{print $1,$2,$3}' Input_file
NOTE: Had a chat with user in room and got to know why this code was not working for user because of gunzip -c file was being used wrongly, its output was being saved into a variable on which user was running awk program, so correcting that command generated right file and awk program ran fine on it. Adding this as a reference for future readers.
One approach would be:
awk -v FS="," -v OFS="|~|" '{gsub(/[|][~][|]/,","); sub(/^\s*/,""); print $1,$2,$3}' file1.txt
The approach simply replaces all "|~|" with a "," setting the output file separator to "|~|". All leading whitespace is trimmed with sub().
Example Use/Output
With your data in file1.txt, you would have:
$ awk -v FS="," -v OFS="|~|" '{gsub(/[|][~][|]/,","); sub(/^\s*/,""); print $1,$2,$3}' file1.txt
a|~|b|~|c
1|~|2|~|3
11|~|22|~|33
111|~|222|~|333
Let me know if this is what you intended. You can simply redirect, e.g. > file2.txt to write to the second file.
For such cases, my bash+awk script rcut comes in handy:
rcut -Fd'|~|' -f-3 ip.txt
The -F option enables fixed string input delimiter (which is given using the -d option). And by default, the output field separator will also be same as -d when -F is active. -f-3 is similar to cut syntax to specify first three fields.
For better speed, use hck command:
hck -Ld'|~|' -D'|~|' -f-3 ip.txt
Here, -L enables literal field separator and -D specifies output field separator.
Another benefit is that hck supports -z option to automatically handle common compressed formats based on filename extension (adding this since OP had an issue with compressed input).
Another way:
sed 's/|~|/\t/g' file1.txt | awk '{print $1"|~|"$2"|~|"$3}' > file2.txt
First replace the |~| delimiter, and use the default awk separator, then print columns what you need.
I am working with bash script that has this command in it.
awk -F ‘‘ ‘/abc/{print $3}’|xargs
What is the meaning of this command?? Assume input is provided to awk.
The quick answer is it'll do different things depending on the version of awk you're running and how many fields of output the awk script produces.
I assume you meant to write:
awk -F '' '/abc/{print $3}'|xargs
not the syntactically invalid (due to "smart quotes"):
awk -F ‘’’/abc/{print $3}’|xargs
-F '' is undefined behavior per POSIX so what it will do depends on the version of awk you're running. In some awks it'll split the current line into 1 character per field. in others it'll be ignored and the line will be split into fields at every sequence of white space. In other awks still it could do anything else.
/abc/ looks for a string matching the regexp abc on the current line and if found invokes the subsequent action, in this case {print $3}.
However it's split into fields, print $3 will print the 3rd such field.
xargs as used will just print chunks of the multi-line input it's getting all on 1 line so you could get 1 line of all-fields output if you don't have many fields being output or several lines of multi-field output if you do.
I suspect the intent of that code was to do what this code actually will do in any awk alone:
awk '/abc/{printf "%s%s", sep, substr($0,3,1); sep=OFS} END{print ""}'
e.g.:
$ printf 'foo\nxabc\nyzabc\nbar\n' |
awk '/abc/{printf "%s%s", sep, substr($0,3,1); sep=OFS} END{print ""}'
b a
I am using two commands:
awk '{ print $2 }' SomeFile.txt > Pattern.txt
grep -f Pattern.txt File.txt
With the first command I create a list of desirable patterns. With the second command I extract all lines in File.txt that match the lines in the Pattern.txt
My question is, is there a way to combine awk and grep in a pipeline so that I don't have to generate the intermediate Pattern.txt file?
Thanks!
You can do this all in one invocation of awk:
awk 'NR==FNR{a[$2];next}{for(i in a)if($0~i)print}' Somefile.txt File.txt
Populate keys in the array a from the second column of the first file. NR==FNR identifies the first file (total record number is equal to this file's record number). next skips the second block for the first file.
In the second block, loop through all the keys in the array and if the line matches any of them, print it. To avoid printing the line more than once if it matches more than one pattern, you could add a next here too, i.e. {for(i in a)if($0~i){print;next}}.
If the "patterns" are actually fixed strings, it is even simpler:
awk 'NR==FNR{a[$2];next}$0 in a' Somefile.txt File.txt
If your shell supports it, you can use process substitution:
grep -f <(awk '{ print $2 }' SomeFile.txt) File.txt
bash and zsh will support that, others will probably too, didn't tested.
Simpler as the above and supported by all shells would be to use a pipe:
awk '{ print $2 }' SomeFile.txt | grep -f - File.txt
- is used as the argument to -f. - has a special meaning here and stands for stdin. Thanks to Tom Fenech for mentioning that!
I`m working on a set of data for which I need specific fields as output:
The data looks like this:
/home/oracle/db.log.gz:2013-1-19T00:00:25 <user.info> 1 2013-1-19T00:00:53.911 host_name RT_FLOW [junos#26.1.1.1.2.4 source-address="10.1.2.0" source-port="616" destination-address="100.1.1.2" destination-port="23" service-name="junos-telnet" nat-source-address="20x.2x.1.2" nat-source-port="3546" nat-destination-address="9x.12x.3.0"]
From above I need three things:
(I) - 2013-1-19T00:00:53.911 which is $4
(II)- source-address="10.1.2.0" which is $8 of which I need only 10.1.2.0
(III) - destination-address="100.1.1.2" which $10 of which I need only 100.1.1.2
I cannot use simple awk like this -> awk '{ print $4 \t $8 \t $10 }' since there are some fields after "device_name" in the log file which are not always present in all log lines so I have to make use of delimiters such as
awk -F 'source-address=' '{print $2}' | awk '{print $1} -> this gives source-addressIP which is (II) requirement
I`m not sure how do I combine using a awk search for I and II and III.
Can someone help?
I believe sed is better for this job
sed -r 's/([^ ]+[ ]+){3}([^ ]+).*[ ]+source-address="([^"]+)".*[ ]+destination-address="([^"]+)".*/\2\t\3\t\4/' file
Output:
2013-1-19T00:00:53.911 10.1.2.0 100.1.1.2
What do you exactly want?
solve the problem using any (reasonably standard) tool
solve this challenge using one instance of awk
solve the problem using just awk, no matter how many instances it costs
For the first case, you could parse the line using scripting language of your choice (mine would be Perl), or do it the hard way using sed and a single big substitution. Or something between the two – use three regexes to get the parts you want.
For the second case, you could adapt any of the former solutions, preferably the sed one. Awk and sed solutions have already been posted.
For the third case, you could just run the obvious awk solutions you mentioned in your question and send the results to a single pipe like { awk …; awk …; awk …; } < file | consumer.
Try doing this :
awk '{print gensub(/.*\s+([0-9]{4}-[0-9]+-[0-9]+T[0-9]{2}:[0-9]{2}:[0-9]{2}.[0-9]+).*source-address="([0-9]{1,3}\.[0-9]{1,3}\.[0-9]{1,3}\.[0-9]{1,3}).*destination-address="([0-9]{1,3}\.[0-9]{1,3}\.[0-9]{1,3}\.[0-9]{1,3}).*/, "(I) \\1\n(II) \\2\n(III) \\3", "g"); }' file
Another solution using perl :
perl -lne 'print "(", "I" x ++$c, ") $_" for m/.*?\s+(\d{4}-\d+-\d+T\d{2}:\d{2}:\d{2}.\d+).*source-address="(\d{1,3}\.\d{1,3}\.\d{1,3}\.\d{1,3}).*destination-address="(\d{1,3}\.\d{1,3}\.\d{1,3}\.\d{1,3}).*/' file
Outputs :
(I) 2013-1-19T00:00:53.911
(II) 10.1.2.0
(III) 100.1.1.2