I have to use bash to iterate over a CSV file and replace the values of a column that meets a condition. Finally, the results have to be stored in an output file.
I have written this code, which reads the file and stores the content in an array. On iterating over the file, if the value at column 13 is equal to "NULL" then the value of this record has to be replaced by "0". Once the file is reviewed the output with the replaced values is stored at file_b.
#!/bin/bash
file="./2022_Accidentalidad.csv"
while IFS=; read -ra array
do
if [[ ${array[13]} == "NULL" ]]; then
echo "${array[13]}" | sed -n 's/NULL/0/g'
fi
done < $file > file_b.csv
The problem is that file_b is empty. Nothing is written there.
How could I do this?
I cannot use AWK, and have to use or a FOR or a WHILE command to iterate over the file.
Sample input:
num_expediente;fecha;hora;localizacion;numero;cod_distrito;distrito;tipo_accidente;estado_meteorológico;tipo_vehiculo;tipo_persona;rango_edad;sexo;cod_lesividad;lesividad;coordenada_x_utm;coordenada_y_utm;positiva_alcohol;positiva_droga
2022S000001;01/01/2022;1:30:00;AVDA. ALBUFERA, 19;19;13;PUENTE DE VALLECAS;Alcance;Despejado;Turismo;Conductor;De 18 a 30 años;Mujer;NULL;NULL;443359,226;4472082,272;N;NULL
Expected output
num_expediente;fecha;hora;localizacion;numero;cod_distrito;distrito;tipo_accidente;estado_meteorológico;tipo_vehiculo;tipo_persona;rango_edad;sexo;cod_lesividad;lesividad;coordenada_x_utm;coordenada_y_utm;positiva_alcohol;positiva_droga
2022S000001;01/01/2022;1:30:00;AVDA. ALBUFERA, 19;19;13;PUENTE DE VALLECAS;Alcance;Despejado;Turismo;Conductor;De 18 a 30 años;Mujer;0;NULL;443359,226;4472082,272;N;NULL
Thanks a lot in advance.
You don't need sed. Just replace $array[13] with 0. Then print the entire array with ; separators between the fields.
( # in a subshell
IFS=';' # set IFS, that affects `read` and `"${array[*]}"`
while read -ra array
do
if [[ ${array[13]} == "NULL" ]]; then
array[13]=0
fi
echo "${array[*]}"
done
) < $file > file_b.csv
echo uses the first character of $IFS as the output field separator.
When awk is also possible:
awk 'BEGIN{FS=OFS=";"} NR==2 && $14=="NULL"{$14=0} {print}' "$file" > file_b.csv
See: 8 Powerful Awk Built-in Variables – FS, OFS, RS, ORS, NR, NF, FILENAME, FNR
One idea using a regex and the BASH_REMATCH array:
regex='(([^;]*;){13})(NULL)(;.*)'
while read -r line
do
[[ "${line}" =~ $regex ]] &&
line="${BASH_REMATCH[1]}0${BASH_REMATCH[4]}"
# uncomment following line to display contents of BASH_REMATCH[] array
# declare -p BASH_REMATCH
echo "${line}"
done < file.csv > file_b.csv
This generates:
$ cat file_b.csv
num_expediente;fecha;hora;localizacion;numero;cod_distrito;distrito;tipo_accidente;estado_meteorológico;tipo_vehiculo;tipo_persona;rango_edad;sexo;cod_lesividad;lesividad;coordenada_x_utm;coordenada_y_utm;positiva_alcohol;positiva_droga
2022S000001;01/01/2022;1:30:00;AVDA. ALBUFERA, 19;19;13;PUENTE DE VALLECAS;Alcance;Despejado;Turismo;Conductor;De 18 a 30 años;Mujer;0;NULL;443359,226;4472082,272;N;NULL
Related
I am attempting to return the line number of lines that have a break. An input example:
2938
383
3938
3
383
33333
But my script is not working and I can't see why. My script:
input="./input.txt"
declare -i count=0
while IFS= read -r line;
do
((count++))
if [ "$line" == $'\n\n' ]; then
echo "$count"
fi
done < "$input"
So I would expect, 3, 6 as output.
I just receive a blank response in the terminal when I execute. So there isn't a syntax error, something else is wrong with the approach I am taking. Bit stumped and grateful for any pointers..
Also "just use awk" doesn't help me. I need this structure for additional conditions (this is just a preliminary test) and I don't know awk syntax.
The issue is that "$line" == $'\n\n' won't match a newline as it won't be there after consuming an empty line from the input, instead you can match an empty line with regex pattern ^$:
if [[ "$line" =~ ^$ ]]; then
Now it should work.
It's also match easier with awk command:
$ awk '$0 == ""{ print NR }' test.txt
3
6
As Roman suggested, line read by read terminates with a delimiter, and that delimiter would not show up in the line the way you're testing for.
If the pattern you are searching for looks like an empty line (which I infer is how a "double newline" always manifests), then you can just test for that:
while read -r; do
((count++))
if [[ -z "$REPLY" ]]; then
echo "$count"
fi
done < "$input"
Note that IFS is for field-splitting data on lines, and since we're only interested in empty lines, IFS is moot.
Or if the file is small enough to fit in memory and you want something faster:
mapfile -t -O1 foo < i
declare -p foo
for n in "${!foo[#]}"; do
if [[ -z "${foo[$n]}" ]]; then
echo "$n"
fi
done
Reading the file all at once (mapfile) then stepping through an array may be easier on resources than stepping through a file line by line.
You can also just use GNU awk:
gawk -v RS= -F '\n' '{ print (i += NF); i += length(RT) - 1 }' input.txt
By using FS = ".+", it ensures only truly zero-length (i.e. $0 == "") line numbers get printed, while skipping rows consisting entirely of [[:space:]]'s
echo '2938
383
3938
3
383
33333' |
{m,g,n}awk -F'.+' '!NF && $!NF = NR'
3
6
This sed one-liner should do the job at once:
sed -n '/^$/=' input.txt
Simply writes the current line number (the = command) if the line read is empty (the /^$/ matches the empty line).
I have data file which I need to filter with bash script, see data example:
name=pencils
name=apples
value=10
name=rocks
value=3
name=tables
value=6
name=beds
name=cups
value=89
I need to group name value pairs like so apples=10, if current line starts with name and next line starts with name, first line should be omitted entirely. So result file should look like this:
apples=10
rocks=3
tables=6
cups=89
I came with this simple solution which works but is very slow, it takes 5 min to complete for file with 2000 lines.
VALUES=$(cat input.txt)
for x in $VALUES; do
if [[ -n $(echo $x | grep 'name=') ]]; then
name=$(echo $x | sed "s/name=//")
elif [[ -n $(echo $x | grep 'value=') ]]; then
value=$(echo $x | sed "s/value=//")
echo "${name}=${value}" >> output.txt
fi
done
I'm aware that this kind of task is not very suitable for bash, but script is already written and this is just small part of it.
How can I optimize this task in bash?
Do not run any commands in subshells, it slows your script a lot. You can do everything in the current shell.
#! /bin/bash
while IFS== read k v ; do
if [[ $k == name ]] ; then
name=$v
elif [[ $k == value ]] ; then
printf '%s=%s\n' "$name" "$v"
fi
done
There are three easy optimizations you can make that will greatly speed up the script without requiring a major rethink.
1. Replace for with while read
Loading input.txt into a string, and then looping over that string with for x in $VALUES is slow. It requires the whole file to be read into memory even though this task could be done in a streaming fashion, reading a line at a time.
A common replacement for for line in $(cat file) is while read line; do ... done < file. It turns out that loops are compound commands, and like the normal one-line commands we're used to, compound commands can have < and > redirections. Redirecting a file into a loop means that for the duration of the loop, stdin comes from the file. So if you call read line inside the loop then it will read one line each iteration.
while IFS= read -r x; do
if [[ -n $(echo $x | grep 'name=') ]]; then
name=$(echo $x | sed "s/name=//")
elif [[ -n $(echo $x | grep 'value=') ]]; then
value=$(echo $x | sed "s/value=//")
echo "${name}=${value}" >> output.txt
fi
done < input.txt
2. Redirect output outside loop
It's not just input that can be redirected. We can do the same thing for the >> output.txt redirection. Here's where you'll see the biggest speedup. When >> output.txt is inside the loop output.txt must be opened and closed every iteration, which is crazy slow. Moving it to the outside means it only needs to be opened once. Much, much faster.
while IFS= read -r x; do
if [[ -n $(echo $x | grep 'name=') ]]; then
name=$(echo $x | sed "s/name=//")
elif [[ -n $(echo $x | grep 'value=') ]]; then
value=$(echo $x | sed "s/value=//")
echo "${name}=${value}"
fi
done < input.txt > output.txt
3. Shell string processing
One final improvement is to use faster string processing. Calling grep requires forking a subprocess every time just to do a simple string split. It'd be a lot faster if we could do the string splitting using just shell constructs. Well, as it happens that's easy now that we've switched to read. read can do more than read whole lines; it can also split on a delimiter from the variable $IFS (inter-field separator).
while IFS='=' read -r key value; do
case "$key" in
name) name="$value";;
value) echo "$name=$value";;
fi
done < input.txt > output.txt
Further reading
BashFAQ/001 - How can I read a file (data stream, variable) line-by-line (and/or field-by-field)?
This explains why I have IFS= read -r in the first two iterations.
BashFAQ/024 - I set variables in a loop that's in a pipeline. Why do they disappear after the loop terminates? Or, why can't I pipe data to read?
cmd | while read; do ... done is another popular use of while read, but it has unique pitfalls.
BashFAQ/100 - How do I do string manipulations in bash?
More in-shell string processing options.
If you have performance issues do not use bash at all. Use a text processing tool like, for instance, awk:
$ awk -F= '{name = $2} $1 == "value" {print name "=" $2}' data.txt
apples=10
rocks=3
tables=6
cups=89
Explanation: -F= defines the field separator as character =. The first block is executed only if the first field of a line ($1) is equal to string value. It prints variable name followed by character = and the second field ($2). The second block is executed on each line and it stores the second field ($2) in variable name.
Normally, if your input resembles what you show, this should automatically skip the first line. Else, we can exclude it explicitly using a test on the NR variable which value is the line number, starting at 1:
awk -F= 'NR != 1 && $1 == "value" {print name "=" $2}
NR != 1 {name = $2}' data.txt
All this works on inputs like the one you show but not on inputs where you would have other types of lines or several value=... consecutive lines. If you really want to test that the name/value pair is on two consecutive lines we need something more. For instance, test if the first field is name and use another variable n to store the line number of the last encountered name=... line. With all these tests we can now put the 2 blocks in a slightly more intuitive order (but the opposite would work the same):
awk -F= 'NR != 1 && $1 == "name" {name = $2; n = NR}
NR != 1 && NR == n+1 && $1 == "value" {print name "=" $2}' data.txt
With awk there might be a more elegant solution but you can have:
awk 'BEGIN{RS="\n?name=";FS="\nvalue="} {if($2) printf "%s=%s\n",$1,$2}' inputs.txt
RS="\n?name=" says that the record separator is name=
FS="\nvalue=" says that the field separator for each record is value=
if($2) says to only proceed the printf is the second field exists
This question already has answers here:
Bash tool to get nth line from a file
(22 answers)
Closed 7 years ago.
This is my script. It print every row in the file with the number of row.
Next i want to read which row user choosed and save it to some variable.
I=1
for ROW in $(cat file.txt)
do
echo "$I $ROW"
I=`expr $I + 1`
done
read var
awk 'FNR = $var {print}' file.txt
Then i want to to print / save the chosen row into the file.
How can I do this ?
when i echo $var it shows me properly the number. But when i'm trying to use this variable in awk, it print every line.
How to read the 'var' line from file?
And moreover, how to save this line in other variable?
Example file.txt
1 line1
2 line2
3 line3
4 line4
when i tap 3 i want to read third line from file.
Try this:
cat -n file.txt; read var; line="$(sed -n ${var}p file)"; echo "$line"
With more focus on Dryingsoussage's version:
#!/bin/bash
file="file.txt"
declare -i counter=0 # set integer attribute
var=0
while read -r line; do
counter=counter+1
printf "%d %s\n" "$counter" "$line"
done < "$file"
# check for number and greater-than 0 and less-than-or-equal $counter
until [[ $var =~ ^[0-9]+$ ]] && [[ $var -gt 0 ]] && [[ $var -le $counter ]]; do
read -p "Enter line number:" var
done
awk -v var="$var" 'FNR==var {print}' "$file"
You cannot use $varname inside ' ' they will not be resolved.
look at this other post it should help you:
How to use shell variables in an awk script
cat -n file.txt
read var
row="$(awk -v tgt="$var" 'NR==tgt{print;exit}' file.txt)"
First: You cannot use $var in a single quotes, as echo '$var' would be plain $var, no its value.
Second: You used = (assignment) operator instead of == (equality) operator.
Third: You don't have to write { print } if you want the line to be printed. You can write nothing instead.
Fourth: As was explained in the deleted comment below - do not allow bash expanding the variables in the awk script code, as it can lead to code injection.
So conclusion is:
awk -v var="$var" 'FNR == var' file.txt
should do what you want.
I can do this easily in python or some other high level language. What I am interested in is doing this with bash.
Here is the file format:
head-xyz
item1
item2
item3
head-abc
item8
item5
item6
item9
What I would like to do is print the following output:
head-xyz: 3
head-abc: 4
header will have a specific pattern similar to the example i gave above. items also have specific patterns like in the example above. I am only interested in the count of items under each header.
You can use awk:
awk '/head/{h=$0}{c[h]++}END{for(i in c)print i, c[i]-1}' input.file
Breakdown:
/head/{h=$0}
For every line matching /head/, set variable h to record the header.
{c[h]++}
For every line in the file, update the array c, which stores a map from header string to line count.
END{for(i in c)print i, c[i]-1}
At the end, loop through the keys in array c and print the key (header) followed by the value (count). Subtract one to avoid counting the header itself.
Note: Bash version 4 only (uses associative arrays)
#!/usr/bin/env bash
FILENAME="$1"
declare -A CNT
while read -r LINE || [[ -n $LINE ]]
do
if [[ $LINE =~ ^head ]]; then HEADLINE="$LINE"; fi
if [ ${CNT[$HEADLINE]+_} ];
then
CNT[$HEADLINE]=$(( ${CNT[$HEADLINE]} + 1 ))
else
CNT[$HEADLINE]=0
fi
done < "$FILENAME"
for i in "${!CNT[#]}"; do echo "$i: ${CNT[$i]}"; done
Output:
$ bash countitems.sh input
head-abc: 4
head-xyz: 3
Does this answer your question #powerrox ?
If you don't consider sed a high-level language, here's another approach:
for file in head-*; do
echo "$file: \c"
sed -n '/^head-/,${
/^head-/d
/^item[0-9]/!q
p
}
' <$file | wc -l
done
In English, the sed script does
Don't print by default
Within lines matching /^head-/ to end of file
Delete the "head line"
After that, quit if you find a non-item line
Otherwise, print the line
And wc -l to count lines.
Okay, so I have a variable ($line) that is defined in the bash/shell script as
$line = "abc:123:def:345"
need to get this column2 = "123"
How do I extract the value of the 2nd column i.e. "123" and name it as a different variable which can be summed later on? I know you have to separate it based on the delimiter ':' but I don't know how to transfer to different variable whilst taking input from $line variable. I only ask this because for some weird reason my code reads the first line of text file BUT doesn't perform the awk on just the first line only so hence the sum is wrong.
FILE=$1
while read line
do
awk -F: '{summation += $3;}END{print summation;}'
done < $FILE
-code via shell script
Thanks.
You can use awk to get second field:
line="abc:123:def:345"
awk -F: '{print $2}' <<< "$line"
123
To assign a variable in the shell, no $ on the left-hand side, no spaces around the =, and < and > are not valid quote characters
line="abc:123:def:345"
In bash, you would do this:
IFS=: read -ra fields <<< "$line"
temporarily set IFS to a colon
use the $line variable as input to the read command (a here-string)
and read the values into the fields array.
Bash arrays are indexed starting from zero, so to extract the 2nd field:
echo "${fields[1]}" # => 123
way in bash using expr
Line2=$(expr $line : "[^:]*:\([^:]*\)")
or if the fields are always 3 characters
Line2=${line:4:3}
Using plain POSIX features:
#!/usr/bin/env sh
line='abc:123:def:345'
IFS=:
# Split line on IFS into arguments
set -- $line
printf %s\\n "$2"
Alternate method:
#!/usr/bin/env sh
line='abc:123:def:345'
# Strip out first column
a="${line#*:}"
# Strip out remaining columns except 1st
b="${a%%:*}"
printf %s\\n "$b"