I have 2 text files. I want to loop in the first file to get a list, then using that list, loop from the second file to search for matching fields.
The first loop was fine, but when the second loop comes in, the variable $CLIENT_ABBREV cannot be read in the second loop, it's reading as blank. Output looks like does not match DOG where there's a blank before does.
while IFS=',' read CLIENT_ID NAME SERVER_NAME CLIENT_ABBREV
do
echo "\n------------"
echo Configuration in effect for this run
echo CLIENT_ID=$CLIENT_ID
echo NAME=$NAME
echo SERVER_NAME=$SERVER_NAME
echo CLIENT_ABBREV=$CLIENT_ABBREV
while IFS=',' read JOB_NAME CLIENT_ABBREV_FROMCOMMAND JOBTYPE JOBVER
do
if [ "$CLIENT_ABBREV" == "$CLIENT_ABBREV_FROMCOMMAND" ]; then
# do something
else
echo $CLIENT_ABBREV does not match $CLIENT_ABBREV_FROMCOMMAND
done <"$COMMAND_LIST"
done <"$CLIENT_LIST"
Is there a file with the name COMMAND_LIST ?
Or, actually do you want to use $COMMAND_LIST instead of COMMAND_LIST ?
Related
I'm using bash in the WSL (via Terminus) and I'm trying to read in a csv file using the following:
INPUT=student_lookup.csv
IFS=','
[ ! -f $INPUT ] && { echo "$INPUT file not found"; exit 99; }
while read st1 st2
do
fsrc1="./test_rep/*$st1*.org" ;
fsrc1=${fsrc1,,}
fsrc2="./test_rep/*$st2*.org" ;
fsrc2=${fsrc2,,}
echo "$fsrc1"
echo "$fsrc2"
done < $INPUT
The problem is my output looks like:
./test_rep/*AAABBB001*.org
*.orgt_rep/*AAACCC002
./test_rep/*BBBCCC002*.org
*.orgt_rep/*BBBDDD003
The first variable assignment is happening as expected, but I'm confused as to why the second variable is overwriting the start of the variable rather than appending *.org to the end? I'm reading in student numbers (I've changed the letters of the student numbers, but the format is the same).
My input file looks like
1 AAABBB001,AAACCC002
1 BBBCCC002,BBBDDD003
2 CCCDDD003,CCCEEE004
Edit: seems like the dos line endings were the problem
I resolved it by stripping the first 9 letters from the read line, i.e.
fsrc2="./test_rep/*${st2:0:9}*.org" ;
I had what I thought was a simple concept which I could easily do as I did something similar.
I have an input file input.csv
1a,1b
2a,2b
I would like the following output
Output file 1
This is variable 1 named 1a ok
This is variable 2 named 1b ok
Output file 2
This is variable 1 named 2a ok
This is variable 2 named 2b ok
I thought I could do something similar to below
i=1
while IFS=, read var1 var2; do
echo This is variable 1 named "var1" > filenamei
echo This is variable 2 named "var2" >> filenamei
i=i+1
done </inputfile.csv
I previously wrote code to take a single variable from a long file and write output to a single file and it worked fine. Like below
Input file
a
b
Single output file
This is A
This is B
Script was
while read p;do
echo this is "$p" >>output file
done < input file
Been through lots of different errors but getting nowhere.
It will be easy by configuring double loop: the outer loop to iterate over lines and the inner one for comma-separated fields. Then how about:
#!/bin/bash
i=1
while read -r line; do
ifs_back="$IFS"
IFS=","
set -- $line
for ((j=1; j<=$#; j++)); do
echo This is variable "$j" named "${!j}" >> "filename${i}"
done
IFS="$ifs_back"
i=$((i+1))
done < "inputfile.csv"
Explanations:
In order to split the input line with commas, we temporarily set IFS to "," then assign the fields to positional parameters $1, $2.
The loop counter j for the inner loop starts with 1 and ends with $#1, number of fields.
We can access the value of the positional parameter via ${!j}.
As a clean up of the inner loop, we retrieve IFS and increment i for the next line.
The code above is flexible with #lines and #fields so would work with the input:
1a,1b
2a,2b
3a,3b
as wel as with:
1a,1b,1c
2a,2b,2c
3a,3b,3c
Hope this helps.
I am trying to loop through my file and grab the lines in groups of 2. Every data entry in the file contains a header line and then the following line has the data.
I am trying to: Loop through the file, grab every two lines and manipulate them. My current problem is that I am trying to echo the next line in the loop. So every time I hit a header row, it will print the data line (next line) with it.
out="$(cat $1)" #file
file=${out}
iter=0
for line in $file;
do
if [ $((iter%2)) -eq 0 ];
then
#this will be true when it hits a header
echo $line
# I need to echo the next line here
fi
echo "space"
iter=$((iter+1))
done
Here is an example of a possible input file:
>fc11ba964421kjniwefkniojhsdeddb4_runid=65bedc43sdfsdfsdfsd76b7303_read=42_ch=459_start_time=2017-11-01T21:10:05Z <br>
TGAGCTATTATTATCGGCGACTATCTATCTACGACGACTCTAGCTACGACTATCGACTCGACTACSAGCTACTACGTACCGATC
>fd38df1sd6sdf9867345uh43tr8199_runid=65be1fasdfsdfgdsfg4376b7303_read=60_ch=424_start_time=2017-11-01T21:10:06Z <br>
TGAGCTATTATTATCGGCGACTATCTATCTACGACGACTCTAGCTACGACTATCGACTCGACTACSAGCTACTACGTACCGATC
>1d03jknsdfnjhdsf78sd89ds89cc17d_runid=65bedsdfsdfsdf03_read=24_ch=439_start_time=201711-01T21:09:43Z <br>
TGAGCTATTATTATCGGCGACTATCTATCTACGACGACTCTAGCTACGACTATCGACTCGACTACSAGCTACTACGTACCGATC
header lines start with > and data is the lines containing TGACATC
EDIT:
For those asking about the output, based on the original question, I am trying to access the header and data together. Each header and matching data will be processed 6 times. The end goal is to have each header and data pair:
>fc11ba964421kjniwe (original header)
GATATCTAGCTACTACTAT (original data)
translate to:
>F1_fc11ba964421kjniwe
ASNASDKLNASDHGASKNHDLK
>F2_fc11ba964421kjniwe
ASHGASKNHDLKNASDKLNASD
>F3_fc11ba964421kjniwe
KNHDLKNASDKLNASDASHGAS
>R1_fc11ba964421kjniwe
ASHGLKNASDKLNASDASKNHD
>R2_fc11ba964421kjniwe
AKNASDKLNASDSHGASKNHDL
>R3_fc11ba964421kjniwe
SKNHDLKNASDKASHGALNASD
and then the next header and data entry would generate another 6 lines
If you know your records each consist of exactly 2 lines, use the read command twice on each iteration of the while loop.
while IFS= read -r line1; IFS= read -r line2; do
...
done < "$1"
Your for line in $file notation cannot work; in bash, the text after in is a series of values, not an input file. What you're probably looking for is a while read loop that takes the file as standard input. Something like this:
while read -r header; do
# We should be starting with a header.
if [[ $header != >* ]]; then
echo "ERROR: corrupt header: $header" >&2
break
fi
# read the next line...
read -r data
printf '%s\n' "$data" >> data.out
done < "$file"
I don't know what output you're looking for, so I just made something up. This loop enforces header position with the if statement, and prints data lines to an output file.
Of course, if you don't want this enforcement, you could simply:
grep -v '^>' "$file"
to return lines which are not headers.
I need to create Bash script that generates text files named file001.txt through file050.txt
Of those files, all should have this text inserted "This if file number xxx" (where xxx is the assigned file number), except for file007.txt, which needs to me empty.
This is what I have so far..
#!/bin/bash
touch {001..050}.txt
for f in {001..050}
do
echo This is file number > "$f.txt"
done
Not sure where to go from here. Any help would be very appreciated.
#!/bin/bash
for f in {001..050}
do
if [[ ${f} == "007" ]]
then
# creates empty file
touch "${f}.txt"
else
# creates + inserts text into file
echo "some text/file" > "${f}.txt"
fi
done
The continue statement can be used to skip an iteration of a loop and go on to the next -- though since you actually do want to take an operation on file 7 (creating it), it makes just as much sense to have a conditional:
for (( i=1; i<50; i++ )); do
printf -v filename '%03d.txt' "$i"
if (( i == 7 )); then
# create file if it doesn't exist, truncate if it does
>"$filename"
else
echo "This is file number $i" >"$filename"
fi
done
A few words about the specific implementation decisions here:
Using touch file is much slower than > file (since it starts an external command), and doesn't truncate (so if the file already exists it will retain its contents); your textual description of the problem indicates that you want 007.txt to be empty, making truncation appropriate.
Using a C-style for loop, ie. for ((i=0; i<50; i++)), means you can use a variable for the maximum number; ie. for ((i=0; i<max; i++)). You can't do {001..$max}, by contrast. However, this does need meaning to add zero-padding in a separate step -- hence the printf.
Of course, you can costumize the files' name and the text, the key thing is the ${i}. I tried to be clear, but let us know if you don't understand something.
#!/bin/bash
# Looping through 001 to 050
for i in {001..050}
do
if [ ${i} == 007 ]
then
# Create an empty file if the "i" is 007
echo > "file${i}.txt"
else
# Else create a file ("file012.txt" for example)
# with the text "This is file number 012"
echo "This is file number ${i}" > "file${i}.txt"
fi
done
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