If I have a script which takes three arguments like so:
./myScript.sh path file col1,col3
and if file is like:
id,role,salary
05,engineer,45000
How would I split $3 into separate variables (note that this could be any number of variables, if I had a larger CSV file) in order to only print the corresponding columns to $3.
I've tried saving $3 to a variable, using Tr and array to possible equate the index of the array to the column header number. I failed to do this. What is the most simplistic amateurish approach to resolving this? It would be straight forward if the script took the columns as separate arguments, but when combined in one argument, it's complicating this quite a bit for me.
Expected output:
id,salary
05,45000
If the order of the columns must stay the same:
#!/bin/bash
path="$1"
fname="$2"
cols="$3"
header=($(head -1 "$fname" | sed 's/,/ /g'))
for i in "${!header[#]}"; do
cols=$(echo "$cols" | sed "s/${header[$i]}/$((i+1))/g")
done
cut -d',' -f$cols $fname
If you need more flexibility e.g. define the order of columns, just change the last part of the script with this:
for i in "${!header[#]}"; do
cols=$(echo "$cols" | sed -e "s/${header[$i]}/\$$((i+1))/g")
done
awk -F, "{print(${cols//,/\",\"})}" $fname
Output:
$ ./so.sh <path> input.txt id,salary
id,salary
05,45000
With the awk method, you can do stuff like
$ ./so.sh <path> input.txt id,salary,id,salary
id,salary,id,salary
05,45000,05,45000
I have a large file with 100k lines and about 22 columns. I would like to remove all lines in which the content in column 15 only appears once. So as far as I understand its the reverse of
sort -u file.txt
After the lines that are unique in column 15 are removed, I would like to shuffle all lines again, so nothing is sorted. For this I would use
shuf file.txt
The resulting file should include only lines that have at least one duplicate (in column 15) but are in a random order.
I have tried to work around sort -u but it only sorts out the unique lines and discards the actual duplicates I need. However, not only do I need the unique lines removed, I also want to keep every line of a duplicate, not just one representitive for a duplicate.
Thank you.
Use uniq -d to get a list of all the duplicate values, then filter the file so only those lines are included.
awk -F'\t' 'NR==FNR { dup[$0]; next; }
$15 in dup' <(awk -F'\t' '{print $15}' file.txt | sort | uniq -d) file.txt > newfile.txt
awk '{print $15}' file.txt | sort | uniq -d returns a list of all the duplicate values in column 15.
The NR==FNR line in the first awk script turns this into an associative array.
The second line processes file.txt and prints any lines where column 15 is in the array.
Below is my file 1 content:
123|yid|def|
456|kks|jkl|
789|mno|vsasd|
and this is my file 2 content
123|abc|def|
456|ghi|jkl|
789|mno|pqr|
134|rst|uvw|
The only thing I want to compare in File 1 based on File 2 is column 1. Based on the files above, the output should only output:
134|rst|uvw|
Line to Line comparisons are not the answer since both column 2 and 3 contains different things but only column 1 contains the exact same thing in both files.
How can I achieve this?
Currently I'm using this in my code:
#sort FILEs first before comparing
sort $FILE_1 > $FILE_1_sorted
sort $FILE_2 > $FILE_2_sorted
for oid in $(cat $FILE_1_sorted |awk -F"|" '{print $1}');
do
echo "output oid $oid"
#for every oid in FILE 1, compare it with oid FILE 2 and output the difference
grep -v diff "^${oid}|" $FILE_1 $FILE_2 | grep \< | cut -d \ -f 2 > $FILE_1_tmp
You can do this in Awk very easily!
awk 'BEGIN{FS=OFS="|"}FNR==NR{unique[$1]; next}!($1 in unique)' file1 file2
Awk works by processing input lines one at a time. And there are special clauses which Awk provides, BEGIN{} and END{} which encloses actions to be run before and after the processing of the file.
So the part BEGIN{FS=OFS="|"} is set before the file processing happens, and FS and OFS are special variables in Awk which stand for input and output field separators. Since you have a provided a file that is de-limited by | you need to parse it by setting FS="|" also to print it back with |, so set OFS="|"
The main part of the command comes after BEGIN clause, the part FNR==NR is meant to process the first file argument provided in the command, because FNR keeps track of the line numbers for the both the files combined and NR for only the current file. So for each $1 in the first file, the values are hashed into the array called unique and then when the next file processing happens, the part !($1 in unique) will drop those lines in second file whose $1 value is not int the hashed array.
Here is another one liner that uses join, sort and grep
join -t"|" -j 1 -a 2 <(sort -t"|" -k1,1 file1) <(sort -t"|" -k1,1 file2) |\
grep -E -v '.*\|.*\|.*\|.*\|'
join does two things here. It pairs all lines from both files with matching keys and, with the -a 2 option, also prints the unmatched lines from file2.
Since join requires input files to be sorted, we sort them.
Finally, grep removes all lines that contain more than three fields from the output.
I have a number of tsv files, and I want to check that each file is correctly formatted. primarily, I want to check that each row has the right number of columns. is there a way to do this? I'd love a command line solution if there is one.
Adding this here because these answers were all close but didn't quite work for me, in my case I needed to specify the field separator for awk.
The following should return with a single line containing the number of columns (if every row has the same number of columns).
$ awk -F'\t' '{print NF}' test.tsv | sort -nu
8
-F is used to specify the field separator for awk
NF is the number of fields
-nu orders the field count for each row numerically and returns only the unique ones
If you get more than one row returned, then there are some rows of your .tsv with more columns than others.
To check that the .tsv is correctly formatted with each row having the same number of fields, the following should return 1 (as commented by kmace on the accepted answer) however I needed to add the -F'\t'
$ awk -F'\t' '{print NF}' test.tsv | sort -nu | wc -l
awk '{print NF}' test | sort -nu | head -n 1
This gives you the lowest number of columns in the file on any given row.
awk '{print NF}' test | sort -nu | tail -n 1
This gives you the highest number of columns in the file on any given row.
The result should be the same, if all the columns are present.
Note: this gives me an error on OS X, but not on Debian... maybe use gawk.
(I'm assuming that by "tsv", you mean a file whose columns are separated with tab characters.)
You can do this simply with awk, as long as the file doesn't have quoted fields containing tab characters.
If you know how many columns you expect, the following will work:
awk -F '\t' -v NCOLS=42 'NF!=NCOLS{printf "Wrong number of columns at line %d\n", NR}'
(Of course, you need to change the 42 to the correct value.)
You could also automatically pick up the number of columns from the first line:
awk -F '\t' 'NR==1{NCOLS=NF};NF!=NCOLS{printf "Wrong number of columns at line %d\n", NR}'
That will work (with a lot of noise) if the first line has the wrong number of columns, but it would fail to detect a file where all the lines have the same wrong number of columns. So you're probably better off with the first version, which forces you to specify the column count.
Just cleaning up #snd answer above:
number_uniq_row_lengths=`awk '{print NF}' $pclFile | sort -nu | wc -l`
if [ $number_uniq_row_lengths -eq 1 ] 2>/dev/null; then
echo "$pclFile is clean"
fi
awk is a good candidate for this. If your columns are separated by tabs (I guess it is what tsv means) and if you know how many of them you should have, say 17, you can try:
awk -F'\t' 'NF != 17 {print}' file.tsv
This will print all lines in file.tsv that has not exactly tab-separated 17 columns. If my guess is incorrect, please edit your question and add the missing information (column separators, number of columns...) Note that the tsv (and csv) format is trickier than it seems. The fields can contain the field separator, records can span on several lines... If it is your case, do not try to reinvent the wheel and use an existing tsv parser.
Say I have file - a.csv
ram,33,professional,doc
shaym,23,salaried,eng
Now I need this output (pls dont ask me why)
ram,doc,doc,
shayam,eng,eng,
I am using cut command
cut -d',' -f1,4,4 a.csv
But the output remains
ram,doc
shyam,eng
That means cut can only print a Field just one time. I need to print the same field twice or n times.
Why do I need this ? (Optional to read)
Ah. It's a long story. I have a file like this
#,#,-,-
#,#,#,#,#,#,#,-
#,#,#,-
I have to covert this to
#,#,-,-,-,-,-
#,#,#,#,#,#,#,-
#,#,#,-,-,-,-
Here each '#' and '-' refers to different numerical data. Thanks.
You can't print the same field twice. cut prints a selection of fields (or characters or bytes) in order. See Combining 2 different cut outputs in a single command? and Reorder fields/characters with cut command for some very similar requests.
The right tool to use here is awk, if your CSV doesn't have quotes around fields.
awk -F , -v OFS=, '{print $1, $4, $4}'
If you don't want to use awk (why? what strange system has cut and sed but no awk?), you can use sed (still assuming that your CSV doesn't have quotes around fields). Match the first four comma-separated fields and select the ones you want in the order you want.
sed -e 's/^\([^,]*\),\([^,]*\),\([^,]*\),\([^,]*\)/\1,\4,\4/'
$ sed 's/,.*,/,/; s/\(,.*\)/\1\1,/' a.csv
ram,doc,doc,
shaym,eng,eng,
What this does:
Replace everything between the first and last comma with just a comma
Repeat the last ",something" part and tack on a comma. Voilà!
Assumptions made:
You want the first field, then twice the last field
No escaped commas within the first and last fields
Why do you need exactly this output? :-)
using perl:
perl -F, -ane 'chomp($F[3]);$a=$F[0].",".$F[3].",".$F[3];print $a."\n"' your_file
using sed:
sed 's/\([^,]*\),.*,\(.*\)/\1,\2,\2/g' your_file
As others have noted, cut doesn't support field repetition.
You can combine cut and sed, for example if the repeated element is at the end:
< a.csv cut -d, -f1,4 | sed 's/,[^,]*$/&&,/'
Output:
ram,doc,doc,
shaym,eng,eng,
Edit
To make the repetition variable, you could do something like this (assuming you have coreutils available):
n=10
rep=$(seq $n | sed 's:.*:\&:' | tr -d '\n')
< a.csv cut -d, -f1,4 | sed 's/,[^,]*$/'"$rep"',/'
Output:
ram,doc,doc,doc,doc,doc,doc,doc,doc,doc,doc,
shaym,eng,eng,eng,eng,eng,eng,eng,eng,eng,eng,
I had the same problem, but instead of adding all the columns to awk, I just used (to duplicate the 2nd column):
awk -v OFS='\t' '$2=$2"\t"$2' # for tab-delimited files
For CSVs you can just use
awk -F , -v OFS=, '$2=$2","$2'