Related
I am trying to read values from a CSV file dynamically based on the header. Here's how my input files can look like.
File 1:
name,city,age
john,New York,20
jane,London,30
or
File 2:
name,age,city,country
john,20,New York,USA
jane,30,London,England
I may not be following the best way to accomplish this but I tried the following code.
#!/bin/bash
{
read -r line
line=`tr ',' ' ' <<< $line`
while IFS=, read -r `$line`
do
echo $name
echo $city
echo $age
done
} < file.txt
I am expecting the above code read the values of the header as the variable names. I know that the order of columns can be different for the input file. But, I expect the files to have name, city and age columns in the input file. Is this the right approach? If so, what is the fix for the above code if fails with the error - "line7: name: command not found".
The issue is caused by the backticks. Bash will evaluate the contents and replace the backticks with the output from the command it just evaluated.
You can simply use the variable after the read command to achieve what you want:
#!/bin/bash
{
read -r line
line=`tr ',' ' ' <<< $line`
echo "$line"
while IFS=, read -r $line ; do
echo "person: $name -- $city -- $age"
done
} < file.txt
Some notes on your code:
The backtick syntax is legacy syntax, it is now preferred to use $(...) to evaluate commands. The new syntax is more flexible.
You can enable automatic script failure with set -euo pipefail (see here). This will make your script stop if it encounters an error.
You code is currently very sensitive to invalid header data:
with a file like
n ame,age,city,country
john,20,New York,USA
jane,30,London,England
your script (or rather the version in the beginning of my answer) will run without errors but with invalid output.
It is also good practice to quote variables to prevent unwanted splitting.
To make it much more robust, you can change it as follows:
#!/bin/bash
set -euo pipefail
# -e and -o pipefail will make the script exit
# in case of command failure (or piped command failure)
# -u will exit in case a variable is undefined
# (in you case, if the header is invalid)
{
read -r line
readarray -d, -t header < <(printf "%s" "$line")
# using an array allows to detect if one of the header entries
# contains an invalid character
# the printf is needed because bash would add a newline to the
# command input if using heredoc (<<<).
while IFS=, read -r "${header[#]}" ; do
echo "$name"
echo "$city"
echo "$age"
done
} < file.txt
A slightly different approach can let awk handle the field separation and ordering of the desired output given either of the input files. Below awk stores the desired output order in the f[] (field) array set in the BEGIN rule. Then on the first line in a file (FNR==1) the array a[] is deleted and filled with the headings from the current file. At that point you just loop over the field names in-order in the f[] array and output the corresponding field from the current line, e.g.
awk -F, '
BEGIN { f[1]="name"; f[2]="city"; f[3]="age" } # desired order
FNR==1 { # on first line read header
delete a # clear a array
for (i=1; i<=NF; i++) # loop over headings
a[$i] = i # index by heading, val is field no.
next # skip to next record
}
{
print "" # optional newline between outputs
for (i=1; i<=3; i++) # loop over desired field order
if (f[i] in a) # validate field in a array
print $a[f[i]] # output fields value
}
' file1 file2
Example Use/Output
In your case with the content you show in file1 and file2, you would have:
$ awk -F, '
> BEGIN { f[1]="name"; f[2]="city"; f[3]="age" } # desired order
> FNR==1 { # on first line read header
> delete a # clear a array
> for (i=1; i<=NF; i++) # loop over headings
> a[$i] = i # index by heading, val is field no.
> next # skip to next record
> }
> {
> print "" # optional newline between outputs
> for (i=1; i<=3; i++) # loop over desired field order
> if (f[i] in a) # validate field in a array
> print $a[f[i]] # output fields value
> }
> ' file1 file2
john
New York
20
jane
London
30
john
New York
20
jane
London
30
Where both files are read and handled identically despite having different field orderings. Let me know if you have further questions.
If using Bash verison ≥ 4.2, it is possible to use an associative array to capture an arbitrary number of fields with their name as a key:
#!/usr/bin/env bash
# Associative array to store columns names as keys and and values
declare -A fields
# Array to store columns names with index
declare -a column_name
# Array to store row's values
declare -a line
# Commands block consuming CSV input
{
# Read first line to capture column names
IFS=, read -r -a column_name
# Proces records
while IFS=, read -r -a line; do
# Store column values to corresponding field name
for ((i=0; i<${#column_name[#]}; i++)); do
# Fills fields' associative array
fields["${column_name[i]}"]="${line[i]}"
done
# Dump fields for debug|demo purpose
# Processing of each captured value could go there instead
declare -p fields
done
} < file.txt
Sample output with file 1
declare -A fields=([country]="USA" [city]="New York" [age]="20" [name]="john" )
declare -A fields=([country]="England" [city]="London" [age]="30" [name]="jane" )
For older Bash version, without associative array, use indexed column name alternatively:
#!/usr/bin/env bash
# Array to store columns names with index
declare -a column_name
# Array to store values for a line
declare -a value
# Commands block consuming CSV input
{
# Read first line to capture column names
IFS=, read -r -a column_name
# Proces records
while IFS=, read -r -a value; do
# Print record separator
printf -- '--------------------------------------------------\n'
# Print captured field name and value
for ((i=0; i<"${#column_name[#]}"; i++)); do
printf '%-18s: %s\n' "${column_name[i]}" "${value[i]}"
done
done
} < file.txt
Output:
--------------------------------------------------
name : john
age : 20
city : New York
country : USA
--------------------------------------------------
name : jane
age : 30
city : London
country : England
I have a coma delimited csv file named 'itrs.csv' which I want to parse into a matrix or 2d array using a script bash or shell
Loads\PostDate,schedule,seta,eeta,2019-11-05,2019-11-06,2019-11-07,2019-11-08
BANAMEX,7,1:18:10,1:23:45,G,G,C,C
EMEA,5,0:21:00,1:01:00,G,G,G,C
I have tried the following:
declare -A matrix
eval matrix=($(awk -f, itrs.csv))
for ((i=0;i<=2;i++))
do
for ((j=0;j<=$6;j++))
do
echo ${matrix[$i,$j]}" "
done
echo
done
but above code is throwing errors. I also would like to know how to check the number of columns and rows while parsing data because csv file size may change.
Well, you can do this: Create an associative array, iterate over lines and keep the count of the current line, then iterate over the fields and create an associative array with indexes as requested.
i=0
declare -A matrix
while IFS=, read -r -a line; do
for ((j = 0; j < ${#line[#]}; ++j)); do
matrix[$i,$j]=${line[$j]}
done
((i++))
done < itrs.csv
After it declare -p matrix would output:
declare -A matrix=([1,5]="G" [1,4]="G" [1,7]="C" [1,6]="C" [1,1]="7" [1,0]="BANAMEX" [1,3]="1:23:45" [1,2]="1:18:10" [0,4]="2019-11-05" [0,5]="2019-11-06" [0,6]="2019-11-07"[0,7]="2019-11-08" [0,0]="Loads\\PostDate" [0,1]="schedule" [0,2]="seta" [0,3]="eeta" [2,6]="G" [2,7]="C" [2,4]="G"[2,5]="G" [2,2]="0:21:00" [2,3]="1:01:00" [2,0]="EMEA" [2,1]="5" )
See bashfaq How can I read a file (data stream, variable) line-by-line (and/or field-by-field)?
Don't use eval. eval is evil. Don't eval arr=($(..)) unless you know what you are doing. In your case, using eval looks like it has little to zero sense.
The error comes from awk. awk works like awk [options] script [file], you could awk -F, '{print $0}' itrs.csv, but it would make no sense. The itrs.csv is parsed by awk as being the script - as it makes no sense as a awk script, the tool throws an error.
To read for example the first line only separated by comma into an array in bash you can IFS=, line=($(head -n1 itrs.csv)). The -F, affects how awk parses the file, not how bash creates array - for that use IFS.
I have a file links.txt:
1 a.sh
3 b.sh
6 c.sh
4 d.sh
So, if i pass 1,4 as parameters to another file(master.sh), a.sh and d.sh should be stored in a variable.
sed '3!d' would print the 3rd line, but not the line that starts with 3. For that, you need sed '/^3 /!d'. The problem is you can't combine them for more lines, as this means "Delete everything that doesn't start with a 3", which means all other lines will be missed. So, use sed -n '/^3 /p' instead, i.e. don't print by default and tell sed what lines to print, not what lines to delete.
You can loop over the argument and create a sed script from them that prints the lines, then run sed using this output:
#!/bin/bash
file=$1
shift
for id in "$#" ; do
echo "/^$id /p"
done | sed -nf- "$file"
Run as script.sh filename 3 4.
If you want to remove the id from the output, you can either use
cut -f2 -d' '
or you can modify the generated sed script to do the work
echo "/^$id /s/.* //p"
i.e. only print if the substitution was successful.
This loops through each argument and greps for it in the links file. The result is piped into cut where we specify the delimiter as a space with -d flag and the field number as 2 with -f flag. Finally this is appended to the array called files.
links="links.txt"
files=()
for arg in $#; do
files=("${files[#]}" `grep "^$arg" "$links" | cut -d" " -f2`)
done;
echo ${files[#]}
Usage:
$ ./master.sh 1 4
a.sh d.sh
Edit:
As pointed out by mklement0, the solution above reads the file once per arg. The following first builds the pattern then reads the file just once.
links="links.txt"
pattern="^$1\s"
for arg in ${#:2}; do
pattern+="|^$arg\s"
done
files=$(grep -E "$pattern" "$links" | cut -d" " -f2)
echo ${files[#]}
Usage:
$ ./master.sh 1 4
a.sh d.sh
Here is another example with grep and cut:
#!/bin/bash
for line in $(grep "$1\|$2" links.txt|cut -d' ' -f2)
do
echo $line
done
Example of usage:
./master.sh 1 4
a.sh
d.sh
Why not just stores the values and call them at will:
items=()
while read -r num file
do
items[num]="$file"
done<links.txt
for arg
do
echo "${items[arg]}"
done
Now you can use the items array any time you like :)
The following awk solution:
preserves the argument order; that is, the results reflect the order in which the lookup values were specified (as opposed to the order in which the lookup values happen to occur in the file).
If that is not important (i.e., if outputting the results in file order is acceptable), the readarray technique below can be combined with this one-liner, which is a generalized variant of Panta's answer:
grep -f <(printf "^%s\n" "$#") links.txt | cut -d' ' -f2-
performs well, because the input file is only read once; the only requirement is that all key-value pairs fit into memory as a whole (as a single associative Awk array (dictionary)).
works with any lookup values that don't have embedded whitespace.
Similarly, the assumption is that the output column values (containing values such as a.sh in the sample input) have no embedded whitespace. awk doesn't handle quoted fields well, so more work would be needed.
#!/bin/bash
readarray -t files < <(
awk -v idList="$*" '
BEGIN { count=split(idList, idArr); for (i in idArr) idDict[idArr[i]]++ }
$1 in idDict { idDict[$1] = $2 }
END { for (i=1; i<=count; ++i) print idDict[idArr[i]] }
' links.txt
)
# Print results.
printf '%s\n' "${files[#]}"
readarray -t files reads stdin input (<) line by line into array variable files.
Note: readarray requires Bash v4+; on Bash 3.x, such as on macOS, replace this part with
IFS=$'\n' read -d '' -ra files
<(...) is a Bash process substitution that, loosely speaking, presents the output from the enclosed command as if it were (self-deleting) temporary file.
This technique allows readarray to run in the current shell (as opposed to a subshell if a pipeline had been used), which is necessary for the files variable to remain defined in the remainder of the script.
The awk command breaks down as follows:
-v idList="$*" passes the space-separated list of all command-line arguments as a single string to Awk variable idList.
Note that this assumes that the arguments have no embedded spaces, which is indeed the case here and also generally the case with identifiers.
BEGIN { ... } is only executed once, before the individual lines are processed:
split(idList, idArr) splits the input ID list into an array by whitespace and stores the result in idArr.
for (i in idArr) idDict[idArr[i]]++ } then converts the (conceptually regular) array into associative array idDict (dictionary), whose keys are the input IDs - this enables efficient lookup by ID later, and also allows storing the lookup result for each ID.
$1 in idDict { idDict[$1] = $2 } is processed for every input line:
Pattern $1 in idDict returns true if the line's first whitespace-separated field ($1) - e.g., 6 - is among the keys (in) of associative array idDict, and, if so, executes the associated action ({...}).
Action { idDict[$1] = $2 } then assigns the second field ($2) - e.g., c.sh - to the iDict entry for key $1.
END { ... } is executed once, after all input lines have been processed:
for (i=1; i<=count; ++i) print idDict[idArr[i]] loops over all input IDs in order and prints each ID's lookup result, which is the value of the dictionary entry with that ID.
I have 2 files refer.txt and parse.txt
refer.txt contains the following
julie,remo,rob,whitney,james
parse.txt contains
remo/hello/1.0,remo/hello2/2.0,remo/hello3/3.0,whitney/hello/1.0,julie/hello/2.0,julie/hello/3.0,rob/hello/4.0,james/hello/6.0
Now my output.txt should list the files in parse.txt based on the order specified in refer.txt
ex of output.txt should be:
julie/hello/2.0,julie/hello/3.0,remo/hello/1.0,remo/hello2/2.0,remo/hello3/3.0,rob/hello/4.0,whitney/hello/1.0,james/hello/6.0
i have tried the following code:
sort -nru refer.txt parse.txt
but no luck.
please assist me.TIA
You can do that using gnu-awk:
awk -F/ -v RS=',|\n' 'FNR==NR{a[$1] = (a[$1])? a[$1] "," $0 : $0 ; next}
{s = (s)? s "," a[$1] : a[$1]} END{print s}' parse.txt refer.txt
Output:
julie/hello/2.0,julie/hello/3.0,remo/hello/1.0,remo/hello2/2.0,remo/hello3/3.0,rob/hello/4.0,whitney/hello/1.0,james/hello/6.0
Explanation:
-F/ # Use field separator as /
-v RS=',|\n' # Use record separator as comma or newline
NR == FNR { # While processing parse.txt
a[$1]=(a[$1])?a[$1] ","$0:$0 # create an array with 1st field as key and value as all the
# records with keys julie, remo, rob etc.
}
{ # while processing the second file refer.txt
s = (s)?s "," a[$1]:a[$1] # aggregate all values by reading key from 2nd file
}
END {print s } # print all the values
In pure native bash (4.x):
# read each file into an array
IFS=, read -r -a values <parse.txt
IFS=, read -r -a ordering <refer.txt
# create a map from content before "/" to comma-separated full values in preserved order
declare -A kv=( )
for value in "${values[#]}"; do
key=${value%%/*}
if [[ ${kv[$key]} ]]; then
kv[$key]+=",$value" # already exists, comma-separate
else
kv[$key]="$value"
fi
done
# go through refer list, putting full value into "out" array for each entry
out=( )
for value in "${ordering[#]}"; do
out+=( "${kv[$value]}" )
done
# print "out" array in comma-separated form
IFS=,
printf '%s\n' "${out[*]}" >output.txt
If you're getting more output fields than you have input fields, you're probably trying to run this with bash 3.x. Since associative array support is mandatory for correct operation, this won't work.
tr , "\n" refer.txt | cat -n >person_id.txt # 'cut -n' not posix, use sed and paste
cat person_id.txt | while read person_id person_key
do
print "$person_id" > $person_key
done
tr , "\n" parse.txt | sed 's/(^[^\/]*)(\/.*)$/\1 \1\2/' >person_data.txt
cat person_data.txt | while read foreign_key person_data
do
person_id="$(<$foreign_key)"
print "$person_id" " " "$person_data" >>merge.txt
done
sort merge.txt >output.txt
A text book data processing approach, a person id table, a person data table, merged on a common key field, which is the first name of the person:
[person_key] [person_id]
- person id table, a unique sortable 'id' for each person (line number in this instance, since that is the desired sort order), and key for each person (their first name)
[person_key] [person_data]
- person data table, the data for each person indexed by 'person_key'
[person_id] [person_data]
- a merge of the 'person_id' table and 'person_data' table on 'person_key', which can then be sorted on person_id, giving the output as requested
The trick is to implement an associative array using files, the file name being the key (in this instance 'person_key'), the content being the value. [Essentially a random access file implemented using the filesystem.]
This actually adds a step to the otherwise simple but not very efficient task of grepping parse.txt with each value in refer.txt - which is more efficient I'm not sure.
NB: The above code is very unlikely to work out of the box.
NBB: On reflection, probably a better way of doing this would be to use the file system to create a random access file of parse.txt (essentially an index), and to then consider refer.txt as a batch file, submitting it as a job as such, printing out from the parse.txt random access file the data for each of the names read in from refer.txt in turn:
# 1) index data file on required field
cat person_data.txt | while read data
do
key="$(print "$data" | sed 's/(^[^\/]*)/\1/')" # alt. `cut -d'/' -f1` ??
print "$data" >>./person_data/"$key"
done
# 2) run batch job
cat refer_data.txt | while read key
do
print ./person_data/"$key"
done
However having said that, using egrep is probably just as rigorous a solution or at least for small datasets, I would most certainly use this approach given the specific question posed. (Or maybe not! The above could well prove faster as well as being more robust.)
Command
while read line; do
grep -w "^$line" <(tr , "\n" < parse.txt)
done < <(tr , "\n" < refer.txt) | paste -s -d , -
Key points
For both files, newlines are translated to commas using the tr command (without actually changing the files themselves). This is useful because while read and grep work under the assumption that your records are separated by newlines instead of commas.
while read will read in every name from refer.txt, (i.e julie, remo, etc.) and then use grep to retrieve lines from parse.txt containing that name.
The ^ in the regex ensures matching is only performed from the start of the string and not in the middle (thanks to #CharlesDuffy's comment below), and the -w option for grep allows whole-word matching only. For example, this ensures that "rob" only matches "rob/..." and not "robby/..." or "throb/...".
The paste command at the end will comma-separate the results. Removing this command will print each result on its own line.
I have a file currently in the form
location1 attr attr ... attr
location2 attr attr ... attr
...
locationn attr atrr ... attr
What I want to do is go through each line, grab the location (first field) then iterate through the attributes. So far I know how to grab the first field, but not iterate through the attributes. There are also a different number of attributes for each line.
TEMP_LIST=$DIR/temp.list
while read LINE
do
x=`echo $LINE | awk '{print $1}'`
echo $x
done<$TEMP_LIST
Can someone tell me how to iterate through the attributes?
I want to get the effect like
while read LINE
do
location=`echo $LINES |awk '{print $1}'`
for attribute in attributes
do something involving the $location for the line and each individual $attribute
done<$TEMP_LIST
I am currently working in ksh shell, but any other unix shell is fine, I will find out how to translate. I am really grateful if someone could help as it would save me alot of time.
Thank you.
Similar to DreadPirateShawn's solution, but a bit simpler:
while read -r location all_attrs; do
read -ra attrs <<< "$all_attrs"
for attr in "${attrs[#]}"; do
: # do something with $location and $attr
done
done < inputfile
The second read line makes use of bash's herestring feature.
This might work in other shells too, but here's an approach that works in Bash:
#!/bin/bash
TEMP_LIST=temp.list
while read LINE
do
# Split line into array using space as delimiter.
IFS=' ' read -a array <<< $LINE
# Use first element of array as location.
location=${array[0]}
echo "First param: $location"
# Remove first element from array.
unset array[0]
# Loop through remaining array elements.
for i in "${array[#]}"
do
echo " Value: $i"
done
done < $TEMP_LIST
As you're already using awk in your posted code, why not learn how to use awk, as it is designed for this sort of problem.
while read LINE
do
location=`echo $LINES |awk '{print $1}'`
for attribute in attributes
do something involving the $location for the line and each individual $attribute
done<$TEMP_LIST
is written in awk as
#!/bin/bash
tempList="MyTempList.txt"
awk '{ # implied while loop for input records by default
location=$1
print "location=" location # location as a "header"
for (i=2;i<NF;i++) {
printf("attr%d=%s\t", i, $i) # print each attr with its number
}
printf("\n") # add new-line char to end of each line of attributes
}' ${tempList}
If you want to save your output, use awk '{.....}' ${tempList}> ${tempList}.new
Awk has numerous vars that it sets as it reads your files. NF mean NumberOfFields for the current line. So the for loop, starts at field 2, and prints all remaining fields on that line in the format provided (change to suit your needs). The i<=NF drives the ability to print all elems on a line.
Sometimes you'll want the 3rd to last elem on line, so you can perform math on the value stored in NF, like thirdFromLast=$(NF-3). For all variables that are numbers, you can "dereference" it as a value, and ask awk to print the value stored of the $N(th) field. i.e. try
print "thirdFromLast="(NF-3)
print "thirdFromLast="$(NF-3)
... to see the difference that the $ makes on a variable that holds a number.
(For large amounts of data, 1 awk process will be considerably more efficient that using subprocesses to gather parts of files.)
Also work your way through this tutorial grymoire's awk tutorial
IHTH