I need to find a way to count columns from a file OR stdin without using anything except pure bash. What I have so far...
input="${1:-/dev/stdin}"
rows=0
while read -r myLine
do
a=($myLine)
cols=(${#a[*]})
rows=`expr $rows + 1`
done < $input
echo -e "$rows $cols"
I'm counting both rows and columns. Right now, my column count only works for files, not stdin.
Any advice?
Im running the following commands
echo -e "1\t2\n3\t4" > m1, ./matrix m1
echo -e "1\t2\n3\t4" | matrix
I would advise awk for this task, but if you need bash, you could use arrays:
let c=0
while read -r myLine; do
a=($myLine)
echo "Line $((++c)) has ${#a[*]} columns"
done < file
The array a is filled with the content of the line read by the read function.
The number of columns is the length of the array a.
Note this script assumes the input field separator IFS to be unset (and as a consequence to default to <space><tab><newline> for the read command).
Related
this is probably a very simple question. I looked at other answers but couldn't come up with a solution. I have a 365 line date file. file as below,
01-01-2000
02-01-2000
I need to read this file line by line and assign each day to a separate variable. like this,
d001=01-01-2000
d002=02-01-2000
I tried while read commands but couldn't get them to work.It takes a lot of time to shoot one by one. How can I do it quickly?
Trying to create named variable out of an associative array, is time waste and not supported de-facto. Better use this, using an associative array:
#!/bin/bash
declare -A array
while read -r line; do
printf -v key 'd%03d' $((++c))
array[$key]=$line
done < file
Output
for i in "${!array[#]}"; do echo "key=$i value=${array[$i]}"; done
key=d001 value=01-01-2000
key=d002 value=02-01-2000
Assumptions:
an array is acceptable
array index should start with 1
Sample input:
$ cat sample.dat
01-01-2000
02-01-2000
03-01-2000
04-01-2000
05-01-2000
One bash/mapfile option:
unset d # make sure variable is not currently in use
mapfile -t -O1 d < sample.dat # load each line from file into separate array location
This generates:
$ typeset -p d
declare -a d=([1]="01-01-2000" [2]="02-01-2000" [3]="03-01-2000" [4]="04-01-2000" [5]="05-01-2000")
$ for i in "${!d[#]}"; do echo "d[$i] = ${d[i]}"; done
d[1] = 01-01-2000
d[2] = 02-01-2000
d[3] = 03-01-2000
d[4] = 04-01-2000
d[5] = 05-01-2000
In OP's code, references to $d001 now become ${d[1]}.
A quick one-liner would be:
eval $(awk 'BEGIN{cnt=0}{printf "d%3.3d=\"%s\"\n",cnt,$0; cnt++}' your_file)
eval makes the shell variables known inside your script or shell. Use echo $d000 to show the first one of the newly defined variables. There should be no shell special characters (like * and $) inside your_file. Remove eval $() to see the result of the awk command. The \" quoted %s is to allow spaces in the variable values. If you don't have any spaces in your_file you can remove the \" before and after %s.
I'm working on a long Bash script. I want to read cells from a CSV file into Bash variables. I can parse lines and the first column, but not any other column. Here's my code so far:
cat myfile.csv|while read line
do
read -d, col1 col2 < <(echo $line)
echo "I got:$col1|$col2"
done
It's only printing the first column. As an additional test, I tried the following:
read -d, x y < <(echo a,b,)
And $y is empty. So I tried:
read x y < <(echo a b)
And $y is b. Why?
You need to use IFS instead of -d:
while IFS=, read -r col1 col2
do
echo "I got:$col1|$col2"
done < myfile.csv
To skip a given number of header lines:
skip_headers=3
while IFS=, read -r col1 col2
do
if ((skip_headers))
then
((skip_headers--))
else
echo "I got:$col1|$col2"
fi
done < myfile.csv
Note that for general purpose CSV parsing you should use a specialized tool which can handle quoted fields with internal commas, among other issues that Bash can't handle by itself. Examples of such tools are cvstool and csvkit.
How to parse a CSV file in Bash?
Coming late to this question and as bash do offer new features, because this question stand about bash and because none of already posted answer show this powerful and compliant way of doing precisely this.
Parsing CSV files under bash, using loadable module
Conforming to RFC 4180, a string like this sample CSV row:
12,22.45,"Hello, ""man"".","A, b.",42
should be splitted as
1 12
2 22.45
3 Hello, "man".
4 A, b.
5 42
bash loadable .C compiled modules.
Under bash, you could create, edit, and use loadable c compiled modules. Once loaded, they work like any other builtin!! ( You may find more information at source tree. ;)
Current source tree (Oct 15 2021, bash V5.1-rc3) do contain a bunch of samples:
accept listen for and accept a remote network connection on a given port
asort Sort arrays in-place
basename Return non-directory portion of pathname.
cat cat(1) replacement with no options - the way cat was intended.
csv process one line of csv data and populate an indexed array.
dirname Return directory portion of pathname.
fdflags Change the flag associated with one of bash's open file descriptors.
finfo Print file info.
head Copy first part of files.
hello Obligatory "Hello World" / sample loadable.
...
tee Duplicate standard input.
template Example template for loadable builtin.
truefalse True and false builtins.
tty Return terminal name.
uname Print system information.
unlink Remove a directory entry.
whoami Print out username of current user.
There is an full working cvs parser ready to use in examples/loadables directory: csv.c!!
Under Debian GNU/Linux based system, you may have to install bash-builtins package by
apt install bash-builtins
Using loadable bash-builtins:
Then:
enable -f /usr/lib/bash/csv csv
From there, you could use csv as a bash builtin.
With my sample: 12,22.45,"Hello, ""man"".","A, b.",42
csv -a myArray '12,22.45,"Hello, ""man"".","A, b.",42'
printf "%s\n" "${myArray[#]}" | cat -n
1 12
2 22.45
3 Hello, "man".
4 A, b.
5 42
Then in a loop, processing a file.
while IFS= read -r line;do
csv -a aVar "$line"
printf "First two columns are: [ '%s' - '%s' ]\n" "${aVar[0]}" "${aVar[1]}"
done <myfile.csv
This way is clearly the quickest and strongest than using any other combination of bash builtins or fork to any binary.
Unfortunely, depending on your system implementation, if your version of bash was compiled without loadable, this may not work...
Complete sample with multiline CSV fields.
Conforming to RFC 4180, a string like this single CSV row:
12,22.45,"Hello ""man"",
This is a good day, today!","A, b.",42
should be splitted as
1 12
2 22.45
3 Hello "man",
This is a good day, today!
4 A, b.
5 42
Full sample script for parsing CSV containing multilines fields
Here is a small sample file with 1 headline, 4 columns and 3 rows. Because two fields do contain newline, the file are 6 lines length.
Id,Name,Desc,Value
1234,Cpt1023,"Energy counter",34213
2343,Sns2123,"Temperatur sensor
to trigg for alarm",48.4
42,Eye1412,"Solar sensor ""Day /
Night""",12199.21
And a small script able to parse this file correctly:
#!/bin/bash
enable -f /usr/lib/bash/csv csv
file="sample.csv"
exec {FD}<"$file"
read -ru $FD line
csv -a headline "$line"
printf -v fieldfmt '%-8s: "%%q"\\n' "${headline[#]}"
numcols=${#headline[#]}
while read -ru $FD line;do
while csv -a row "$line" ; (( ${#row[#]} < numcols )) ;do
read -ru $FD sline || break
line+=$'\n'"$sline"
done
printf "$fieldfmt\\n" "${row[#]}"
done
This may render: (I've used printf "%q" to represent non-printables characters like newlines as $'\n')
Id : "1234"
Name : "Cpt1023"
Desc : "Energy\ counter"
Value : "34213"
Id : "2343"
Name : "Sns2123"
Desc : "$'Temperatur sensor\nto trigg for alarm'"
Value : "48.4"
Id : "42"
Name : "Eye1412"
Desc : "$'Solar sensor "Day /\nNight"'"
Value : "12199.21"
You could find a full working sample there: csvsample.sh.txt or
csvsample.sh.
Note:
In this sample, I use head line to determine row width (number of columns). If you're head line could hold newlines, (or if your CSV use more than 1 head line). You will have to pass number or columns as argument to your script (and the number of head lines).
Warning:
Of course, parsing CSV using this is not perfect! This work for many simple CSV files, but care about encoding and security!! For sample, this module won't be able to handle binary fields!
Read carefully csv.c source code comments and RFC 4180!
From the man page:
-d delim
The first character of delim is used to terminate the input line,
rather than newline.
You are using -d, which will terminate the input line on the comma. It will not read the rest of the line. That's why $y is empty.
We can parse csv files with quoted strings and delimited by say | with following code
while read -r line
do
field1=$(echo "$line" | awk -F'|' '{printf "%s", $1}' | tr -d '"')
field2=$(echo "$line" | awk -F'|' '{printf "%s", $2}' | tr -d '"')
echo "$field1 $field2"
done < "$csvFile"
awk parses the string fields to variables and tr removes the quote.
Slightly slower as awk is executed for each field.
In addition to the answer from #Dennis Williamson, it may be helpful to skip the first line when it contains the header of the CSV:
{
read
while IFS=, read -r col1 col2
do
echo "I got:$col1|$col2"
done
} < myfile.csv
If you want to read CSV file with some lines, so this the solution.
while IFS=, read -ra line
do
test $i -eq 1 && ((i=i+1)) && continue
for col_val in ${line[#]}
do
echo -n "$col_val|"
done
echo
done < "$csvFile"
I have a MetaData.csv file that contains many values to perform an analysis. All I want are:
1- Reading column names and making variables similar to column names.
2- Put values in each column into variables as an integer that can be read by other commands. column_name=Its_value
MetaData.csv:
MAF,HWE,Geno_Missing,Inds_Missing
0.05,1E-06,0.01,0.01
I wrote the following codes but it doesn't work well:
#!/bin/bash
Col_Names=$(head -n 1 MetaData.csv) # Cut header (camma sep)
Col_Names=$(echo ${Col_Names//,/ }) # Convert header to space sep
Col_Names=($Col_Names) # Convert header to an array
for i in $(seq 1 ${#Col_Names[#]}); do
N="$(head -1 MetaData.csv | tr ',' '\n' | nl |grep -w
"${Col_Names[$i]}" | tr -d " " | awk -F " " '{print $1}')";
${Col_Names[$i]}="$(cat MetaData.csv | cut -d"," -f$N | sed '1d')";
done
Output:
HWE=1E-06: command not found
Geno_Missing=0.01: command not found
Inds_Missing=0.01: command not found
cut: 2: No such file or directory
cut: 3: No such file or directory
cut: 4: No such file or directory
=: command not found
Expected output:
MAF=0.05
HWE=1E-06
Geno_Missing=0.01
Inds_Missing=0.01
Problems:
1- I want to use array length (${#Col_Names[#]}) as the final iteration which is 5, but the array index start from 0 (0-4). So MAF column was not captured by the loop. Loop also iterate twice (once 0-4 and again 2-4!).
2- When I tried to call values in variables (echo $MAF), they were empty!
Any solution is really appreciated.
This produces the expected output you posted from the sample input you posted:
$ awk -F, -v OFS='=' 'NR==1{split($0,hdr); next} {for (i=1;i<=NF;i++) print hdr[i], $i}' MetaData.csv
MAF=0.05
HWE=1E-06
Geno_Missing=0.01
Inds_Missing=0.01
If that's not all you need then edit your question to clarify your requirements.
If I'm understanding your requirements correctly, would you please try something like:
#!/bin/bash
nr=1 # initialize input line number to 1
while IFS=, read -r -a ary; do # split the line on "," then assign "ary" to the fields
if (( nr == 1 )); then # handle the header line
col_names=("${ary[#]}") # assign column names
else # handle the body lines
for (( i = 0; i < ${#ary[#]}; i++ )); do
printf -v "${col_names[i]}" "${ary[i]}"
# assign the variable "${col_names[i]}" to the input field
done
# now you can access the values via its column name
echo "Fnames=$Fnames"
echo "MAF=$MAF"
fname_list+=("$Fnames") # create a list of Fnames
fi
(( nr++ )) # increment the input line number
done < MetaData.csv
echo "${fname_list[#]}" # print the list of Fnames
Output:
Fnames=19.vcf.gz
MAF=0.05
Fnames=20.vcf.gz
MAF=
Fnames=21.vcf.gz
MAF=
Fnames=22.vcf.gz
MAF=
19.vcf.gz 20.vcf.gz 21.vcf.gz 22.vcf.gz
The statetemt IFS=, read -a ary is mostly equivalent to your
first three lines; it splits the input on ",", and assigns the
array variable ary to the field values.
There are several ways to use a variable's value as a variable name
(Indirect Variable References). printf -v VarName Value is one of them.
[EDIT]
Based on the OP's updated input file, here is an another version:
#!/bin/bash
nr=1 # initialize input line number to 1
while IFS=, read -r -a ary; do # split the line on "," then assign "ary" to the fields
if (( nr == 1 )); then # handle the header line
col_names=("${ary[#]}") # assign column names
else # handle the body lines
for (( i = 0; i < ${#ary[#]}; i++ )); do
printf -v "${col_names[i]}" "${ary[i]}"
# assign the variable "${col_names[i]}" to the input field
done
fi
(( nr++ )) # increment the input line number
done < MetaData.csv
for n in "${col_names[#]}"; do # iterate over the variable names
echo "$n=${!n}" # print variable name and its value
done
# you can also specify the variable names literally as follows:
echo "MAF=$MAF HWE=$HWE Geno_Missing=$Geno_Missing Inds_Missing=$Inds_Missing"
Output:
MAF=0.05
HWE=1E-06
Geno_Missing=0.01
Inds_Missing=0.01
MAF=0.05 HWE=1E-06 Geno_Missing=0.01 Inds_Missing=0.01
As for the output, the first four lines are printed by echo "$n=${!n}" and the last line is printed by echo "MAF=$MAF ....
You can choose either statement depending on your usage of the variables in the following code.
I don't really think you can implement a robust CSV reader/parser in Bash, but you can implement it to work to some extent with simple CSV files. For example, a very simply bash-implemented CSV might look like this:
#!/bin/bash
set -e
ROW_NUMBER='0'
HEADERS=()
while IFS=',' read -ra ROW; do
if test "$ROW_NUMBER" == '0'; then
for (( I = 0; I < ${#ROW[#]}; I++ )); do
HEADERS["$I"]="${ROW[I]}"
done
else
declare -A DATA_ROW_MAP
for (( I = 0; I < ${#ROW[#]}; I++ )); do
DATA_ROW_MAP[${HEADERS["$I"]}]="${ROW[I]}"
done
# DEMO {
echo -e "${DATA_ROW_MAP['Fnames']}\t${DATA_ROW_MAP['Inds_Missing']}"
# } DEMO
unset DATA_ROW_MAP
fi
ROW_NUMBER=$((ROW_NUMBER + 1))
done
Note that is has multiple disadvantages:
it only works with ,-separated fields (truly "C"SV);
it cannot handle multiline records;
it cannot handle field escapes;
it considers the first row always represents a header row.
This is why many commands may produce and consume \0-delimited data just because this control character may be easier to use. Now what I'm not sure about is whether test is the only external command executed by bash (I believe it is, but it can be probably re-implemented using case so that no external test is executed?).
Example of use (with the demo output):
./read-csv.sh < MetaData.csv
19.vcf.gz 0.01
20.vcf.gz
21.vcf.gz
22.vcf.gz
I wouldn't recommend using this parser at all, but would recommend using a more CSV-oriented tool (Python would probably be the easiest choice to use; + or if your favorite language, as you mentioned, is R, then probably this is another option for you: Run R script from command line ).
I have a coma delimited csv file named 'itrs.csv' which I want to parse into a matrix or 2d array using a script bash or shell
Loads\PostDate,schedule,seta,eeta,2019-11-05,2019-11-06,2019-11-07,2019-11-08
BANAMEX,7,1:18:10,1:23:45,G,G,C,C
EMEA,5,0:21:00,1:01:00,G,G,G,C
I have tried the following:
declare -A matrix
eval matrix=($(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 this code in Elastix2.5 (CentOS):
for variable in $(while read line; do myarray[ $index]="$line"; index=$(($index+1)); echo "$line"; done < prueba);
This extract the values for each line from "prueba" file.
Prueba file contents passwords like this:
Admin1234
Hello543
Chicken5444
Dino6759
3434Cars4
Adminis5555
But, $variable only get values from lines where there are letters, I need that it get NULL values from blank lines. How can I do it?
Your problem is use of a for loop with a command substitution ($(...)); let's look at this simple example:
$ for v in $(echo 'line_1'; echo ''; echo 'line_3'); do echo "$v"; done
line_1
line_3
Note how the empty string produced by the 2nd echo command is effectively discarded.
Analogously, any empty lines produced by your while loop are discarded.
The solution is to avoid for loops altogether for parsing command output:
In your case, simply use only the while loop for iterating over the input file:
while read -r line; do
myarray[index++]="$line"
done < prueba
printf '%s\n' "${myarray[#]}"
-r was added to ensure that read doesn't modify the input (doesn't try to interpret \-prefixed sequences) - this is good practice in general.
Note how incrementing the index was moved directly into the array subscript (index++).
printf '%s\n' "${myarray[#]}" prints all array elements after the file's been read, demonstrating that empty lines were read as well.
You can use is_null function.
is_null($a)
http://php.net/manual/en/function.is-null.php