I dynamically iterate through a csv file and select columns that fit the criteria I need. My CSV is separated by commas.
I save these indexes to an array that looks like
echo "${cols_needed[#]}"
1 3 4 7 8
I then need to write these columns to a new file and I've tried the following cut and awk commands, however, as the array is dynamically created, I cant seem to find the right commands that can select them all at once. I have tried cut, awk and paste commands.
awk -v fields=${cols_needed[#]} 'BEGIN{ n = split(fields,f) }
{ for (i=1; i<=n; ++i) printf "%s%s", $f[i], (i<n?OFS:ORS) }' test.csv
This throws an error as it cannot split the fields unless I hard code them (even then, it can only do 2), split on spaces.
fields="1 2’
I have tried to dynamically create -f parameters, but can only do so with one variable in a loop like so
for item in "${cols_needed[#]}";
do
cat test.csv | cut -f$item
done
which outputs one column at a time.
And I have tried to dynamically create it with commas - input as 1,3,4,7...
cat test.csv | cut -f${cols_needed[#]};
which also does not work!
Any help is appreciated! I understand awk does not work like bash and we cannot pass variables around in the same way. I feel like I'm going around in circles a bit! Thanks in advance.
Your first approach is ok, just:
change -v fields=${cols_needed[#]} to -v fields="${cols_needed[*]}", to pass the array as a single shell word
add FS=OFS="," to BEGIN, after splitting (you want to split on spaces, before FS is changed to ,)
ie. BEGIN {n = split(fields, f); FS=OFS=","}
Also, if there are no commas embedded in quoted csv fields, you can use cut:
IFS=,; cut -d, -f "${cols_needed[*]}" test.csv
If there are embedded commas, you can use gawk's FPAT, to only split fields on unquoted commas.
Here's an example using that.
# prepend $ to each number
for i in "${cols_needed[#]}"; do
fields[j++]="\$$i"
done
IFS=,
gawk -v FPAT='([^,]+)|(\"[^\"]+\")' -v OFS=, "{print ${fields[*]}}"
Injecting shell code in to an awk command is generally not great practice, but it's ok here IMO.
Expanding on my comments re: passing the bash array into awk:
Passing the array in as an awk variable:
$ cols_needed=(1 3 4 7 8)
$ typeset -p cols_needed
declare -a cols_needed=([0]="1" [1]="3" [2]="4" [3]="7" [4]="8")
$ awk -v fields="${cols_needed[*]}" 'BEGIN{n=split(fields,f); for (i=1;i<=n;i++) print i,f[i]}'
1 1
2 3
3 4
4 7
5 8
Passing the array in as a 'file' via process substitution:
$ awk 'FNR==NR{f[++n]=$1;next} END {for (i=1;i<=n;i++) print i,f[i]}' <(printf "%s\n" "${cols_needed[#]}")
1 1
2 3
3 4
4 7
5 8
As for OP's main question of extracting a specific set of columns from a .csv file ...
Borrowing dawg's .csv file:
$ cat file.csv
1,2,3,4,5,6,7,8
11,12,13,14,15,16,17,18
21,22,23,24,25,26,27,28
Expanding on the suggestion for passing the bash array in as an awk variable:
awk -v fields="${cols_needed[*]}" '
BEGIN { FS=OFS=","
n=split(fields,f," ")
}
{ pfx=""
for (i=1;i<=n;i++) {
printf "%s%s", pfx, $(f[i])
pfx=OFS
}
print ""
}
' file.csv
NOTE: this assumes OP has provided a valid list of column numbers; if there's some doubt as to the validity of the input (column) numbers then OP can add some logic to address said doubts (eg, are they integers? are they positive integers? do they reference a field (in file.csv) that actually exists?, etc)
This generates:
1,3,4,7,8
11,13,14,17,18
21,23,24,27,28
Suppose you have this variable in bash:
$ echo "${cols_needed[#]}"
3 4 7 8
And this CSV file:
$ cat file.csv
1,2,3,4,5,6,7,8
11,12,13,14,15,16,17,18
21,22,23,24,25,26,27,28
You can select columns of that csv file in awk this way:
awk '
BEGIN{FS=OFS=","}
FNR==NR{split($0, cols," "); next}
{
s=""
for (e=1;e<=length(cols); e++)
s=e<length(cols) ? s $(cols[e]) OFS : s $(cols[e])
print s
}' <(echo "${cols_needed[#]}") file.csv
Prints:
3,4,7,8
13,14,17,18
23,24,27,28
Or, you can do:
awk -v cw="${cols_needed[*]}" '
BEGIN{FS=OFS=","; split(cw, cols," ")}
{
s=""
for (e=1;e<=length(cols); e++)
s=e<length(cols) ? s $(cols[e]) OFS : s $(cols[e])
print s
}' file.csv
# same output
BTW, you can do this entirely with cut:
cut -d ',' -f $(IFS=, ; echo "${cols_needed[*]}") file.csv
3,4,7,8
13,14,17,18
23,24,27,28
I am trying to convert a file containing a column with scaffold numbers and another one with corresponding individual sites into a bed file which lists sites in ranges. For example, this file ($indiv.txt):
SCAFF SITE
1 1
1 2
1 3
1 4
1 5
3 1
3 2
3 34
3 35
3 36
should be converted into $indiv.bed:
SCAFF SITE-START SITE-END
1 1 5
3 1 2
3 34 36
Currently, I am using the following code but it is super slow so I wanted to ask if anybody could come up with a quicker way??
COMMAND:
for scaff in $(awk '{print $1}' $indiv.txt | uniq)
do
awk -v I=$scaff '$1 == I { print $2 }' $indiv.txt | awk 'NR==1{first=$1;last=$1;next} $1 == last+1 {last=$1;next} {print first,last;first=$1;last=first} END{print first,last}' | sed "s/^/$scaff\t/" >> $indiv.bed
done
DESCRIPTION:
awk '{print $1}' $indiv.txt | uniq #outputs a list with the unique scaffold numbers
awk -v I=$scaff '$1 == I { print $2 }' $indiv.txt #extracts the values from column 2 if the value in the first column equals the variable $scaff
awk 'NR==1{first=$1;last=$1;next} $1 == last+1 {last=$1;next} {print first,last;first=$1;last=first} END{print first,last}' #converts the list of sequential numbers into ranges as described here: https://stackoverflow.com/questions/26809668/collapse-sequential-numbers-to-ranges-in-bash
sed "s/^/$scaff\t/" >> $indiv.bed #adds a column with the respective scaffold number and then outputs the file into $indiv.bed
Thanks a lot in advance!
Calling several programs for each line of the input must be slow. It's usually better to find a way how to process all the lines in one call.
I'd reach for Perl:
tail -n+2 indiv.txt \
| sort -u -nk1,1 -nk2,2 \
| perl -ane 'END {print " $F[1]"}
next if $p[0] == $F[0] && $F[1] == $p[1] + 1;
print " $p[1]\n#F";
} continue { #p = #F;' > indiv.bed
The first two lines sort the input so that the groups are always adjacent (might be unnecessary if your input is already sorted that way); Perl than reads the lines,-a splits each line into the #F array, the #p array is used to keep the previous line: if the current line has the same first element and the second element is greater by 1, we go to the continue section which just stores the current line into #p. Otherwise, we print the last element of the previous section and the first line of the current one. The END block is responsible for printing the last element of the last section.
The output is different from yours for sections that have only a single member.
I have this csv file and I am trying to write shell script to calculate sum of column after doing group by on it. Column number is 11th (STATUS)
My script is
awk -F, 'NR>1{arr[$11]++}END{for (a in arr) print a, arr[a]}' $f > $parentdir/outputfile.csv;
File output expected is
COMMITTED 2
but actual output is just 2.
It prints only count and not group by sum. If I delete any other columns and run same query then it works fine but not with below sample data.
FILE NAME;SEQUENCE NR;TRANSACTION ID;RUN NUMBER;START EDITCREATION;END EDITCREATION;END COMMIT;EDIT DURATION;COMMIT DURATION;HAS DEPENDENCY;STATUS;DETAILS
Buldhana_Refinesource_FG_IW_ETS_000001.xml;1;4a032127-b20d-4fa8-9f4d-7f2999c0c08f;1;20180831130210345;20180831130429638;20180831130722406;140;173;false;COMMITTED;
Buldhana_Refinesource_FG_IW_ETS_000001.xml;2;e4043fc0-3b0a-46ec-b409-748f98ce98ad;1;20180831130722724;20180831130947144;20180831131216693;145;150;false;COMMITTED;
change the FS to ; in your script
awk -F';' 'NR>1{arr[$11]++}END{for (a in arr) print a, arr[a]}' file
COMMITTED 2
You're using wrong field separator. Use
awk -F\;
; must be escaped to use it as a literal. Except this, your approach seems OK.
Besides awk, you may also use
tail -n +2 $f | cut -f11 -d\; | sort | uniq -c
or
datamash --header-in -t \; -g 11 count 11 < $f
to do the same thing.
I might be going about this the wrong way but I have tried every syntax and I am stuck on the closest error I could get to.
I have a log file, in which I want to filter to a set of lines like so:
Files : 1 1 1 1 1
Files : 3 3 4 4 5
Files : 10 4 2 3 1
Files : 254 1 1 1 1
The code I have will get me to this point, however, I want to use awk to perform addition of all of the first numeric column, in this instance giving 268 as the output (then performing a similar task on the other columns).
I have tried to pipe the awk output into a loop to perform the final step, but it won't add the values, throwing an error. I thought it could be due to awk handling the entries as a string, but as bash isn't strongly typed it should not matter?
Anyway, the code is:
x=0;
iconv -f UTF-16 -t UTF-8 "./TestLogs/rbTest.log" | grep "Files :" | grep -v "*.*" | egrep -v "Files : [a-zA-Z]" |awk '{$1=$1}1' OFS="," | awk -F "," '{print $4}' | while read i;
do
$x=$((x+=i));
done
Error message:
-bash: 0=1: command not found
-bash: 1=4: command not found
-bash: 4=14: command not found
-bash: 14=268: command not found
I tried a couple of the different addition syntaxes but I feel this has something to do with what I am trying to feed it than the addition itself.
This is currently just with integer values but I would also be looking to perform it with floats as well.
Any help much appreciated and I am sure there is a less convoluted way to achieve this, still learning.
You can do computations in awk itself:
awk '{for (c=3; c<=NF; c++) sum[c]+=$c} END{printf "Total : ";
for (c=3; c<=NF; c++) printf "%s%s", sum[c], ((c<NF)? OFS:ORS) }' file
Output:
Total : 268 9 8 9 8
Here sum is an associative array that holds sum for each column from #3 onwards.
Command breakup:
for (c=3; c<=NF; c++) # Iterate from 3rd col to last col
sum[c]+=$c # Add each col value into an array sum with index of col #
END # Execute this block after last record
printf "Total : " # Print literal "Total : "
for (c=3; c<=NF; c++) # Iterate from 3rd col to last col
printf "%s%s", # Use printf to format the output as 2 strings (%s%s)
sum[c], # 1st one is sum for the given index
((c<NF)? OFS:ORS) # 2nd is conditional string. It will print OFS if it is not last
# col and will print ORS if it is last col.
(Not an answer, but a formatted comment)
I always get antsy when I see a long pipeline of greps and awks (and seds, etc)
... | grep "Files :" | grep -v "*.*" | egrep -v "Files : [a-zA-Z]" | awk '{$1=$1}1' OFS="," | awk -F "," '{print $4}'
Can be written as
... | awk '/Files : [^[:alpha:]]/ && !/\*/ {print $4}'
Are you using grep -v "*.*" to filter out lines with dots, or lines with asterisks? Because you're achieving the latter.
This statement gives me the count of unique values in column 1:
awk -F ',' '{print $1}' infile1.csv | sort | uniq -c | sort -nr > outfile1.csv
It does what I expected (gives the count (left) of unique values (right) in the column):
117 5
58 0
18 4
14 3
11 1
9 2
However, now I want to create a loop, so it will go through all columns.
I tried:
for i in {1..10}
do
awk -F ',' '{print $$i}' infile.csv | sort | uniq -c | sort -nr > outfile$i.csv
done
This does not do the job (it does produce a file but with much more data). I think that a variable in a print statement, as I tried with print $$i, is not something that works in general, since I did not come across it so far.
I also tried this:
awk -F ',' '{for(i=1;i<=NF;i++) infile.csv | sort | uniq -c | sort -nr}' > outfile$i.csv
But this does not give any result at all (meaning syntax errors for infile and sort command). I am sure I am using the for statement the wrong way.
Ideally, I would like the code to find the count of unique values for each column and print them all in the same output file. However, I am already very happy with a well functioning loop.
Please let me know if this explanation is not good enough, I will do my best to clarify.
Any time you write a loop in shell just to manipulate text you have the wrong approach. Just do it in one awk command, something like this using GNU awk for 2D arrays and sorted in (untested since you didn't provide any sample input):
awk -F, '
BEGIN { PROCINFO["sorted_in"] = "#val_num_desc" }
{ for (i=1; i<=NF; i++) cnt[i][$i]++ }
END {
for (i=1; i<=NF; i++)
for (val in cnt[i])
print val, cnt[i][val] > ("outfile" i ".csv")
}
' infile.csv
No need for half a dozen different commands, pipes, etc.
You want to loop through the columns and perform the same command in each one of them. So what you are doing is fine: pass the column name to awk. However, you need to pass the value differently, so that it is an awk variable:
for i in {1..10}
do
awk -F ',' -v col=$i '{print $col}' infile.csv | sort | uniq -c | sort -nr > outfile$i.csv
^^^^^^^^^^^^^^^^^^^^^^^^
done