I am currently making a bash script. The purpose of this script is not important. However, I have a piece of code that is generating an error. The error is as follows:
./script.bs: line 175: read: read error: 0: Key has expired
./script.bs: error reading input file: Key has expired
I have the code below for lines 175-189.
This specific piece of code does the following:
-Reads a txt file, that has a list of targeted files.
-For each targeted file, each line is read. And if that line is contained in $NumbersFile, it will do nothing. If that line is NOT contained in $NumbersFile, it will add that line to NumbersFile.
This general piece of code is working, and added 65810 lines of content to $NumbersFile. It then however got the error I stated above.
I'd like to add that the while loop on line 175 (where the error is happening) is supposed to read about 70'000 lines from the given file.
How do I fix this error so that my script may finish running without a key expired error?
NumbersFile="numbers.txt";
while read line; do
while read gramline; do
has="0";
if grep -Fq -- "$gramline" "$NumbersFile"; then
has="1";
fi
if [ "$has" -eq "0" ]; then
echo "$gramline" >> $NumbersFile;
fi
done < "$line";
done < "targetsfile.txt";
If my comment is accurate, perhaps this might be faster:
{ cat targetsfile.txt; xargs cat < targetsfile.txt; } | sort -u > numbers.txt
Or as clarified:
xargs cat < targetsfile.txt | sort -u > numbers.txt
Notes:
the braces are simply to group the cat and xargs commands so that the combined output can be piped into sort. Documented in the manual at 3.2.4.3 Grouping Commands
The first cat outputs the contents of the "targetsfile.txt" file
the xargs cat < targetsfile.txt construct will execute the cat command for every file listed in the targets file. It's a very concise and efficient way to execute
while IFS= read -r line; do cat "$line"; done < targetsfile.txt
I'm sorry for my poor English, first.
I want to read a file (tel.txt) that contains many tel numbers (a number per line) and use that line to grep command to search about the specific number in the source file (another file)!
I wrote this code :
dir="/home/mujan/Desktop/data/ADSL_CDR_Text_Parts_A"
file="$dir/tel.txt"
datafile="$dir/ADSL_CDR_Like_Tct4_From_960501_to_97501_Part0.txt"
while IFS= read -r line
do
current="$line"
echo `grep -F $current "$datafile" >> output.txt`
done < $file
the tel file sample :
44001547
44001478
55421487
but that code returns nothing!
when I declare 'current' variable with literals it works correctly!
what happened?!
Your grep command is redirected to write its output to a file, so you don't see it on the terminal.
Anyway, you should probably be using the much simpler and faster
grep -Ff "$file" "$datafile"
Add | tee -a output.txt if you want to save the output to a file and see it at the same time.
echo `command` is a buggy and inefficient way to write command. (echo "`command`" would merely be inefficient.) There is no reason to capture standard output into a string just so that you can echo that string to standard output.
Why don't you search for the line var directly? I've done some tests, this script works on my linux (CentOS 7.x) with bash shell:
#!/bin/bash
file="/home/mujan/Desktop/data/ADSL_CDR_Text_Parts_A/tel.txt"
while IFS= read -r line
do
echo `grep "$line" /home/mujan/Desktop/data/ADSL_CDR_Text_Parts_A/ADSL_CDR_Like_Tct4_From_960501_to_97501_Part0.tx >> output.txt`
done < $file
Give it a try... It shows nothing on the screen since you're redirecting the output to the file output.txt so the matching results are saved there.
You should use file descriptors when reading with while loop.instead use for loop to avoid false re-directions
dir="/home/mujan/Desktop/data/ADSL_CDR_Text_Parts_A"
file="$dir/tel.txt"
datafile="$dir/ADSL_CDR_Like_Tct4_From_960501_to_97501_Part0.txt"
for line in `cat $file`
do
current="$line"
echo `grep -F $current "$datafile" >> output.txt`
done
My code is given below. Echo works fine. But, the moment I redirect output of echo to touch, I get an error "no such file or directory". Why ? How do i fix it ?
If I copy paste the output of only echo, then the file is created, but not with touch.
while read line
do
#touch < echo -e "$correctFilePathAndName"
echo -e "$correctFilePathAndName"
done < $file.txt
If you have file names in each line of your input file file.txt then you don't need to do any loop. You can just do:
touch $(<file.txt)
to create all the files in one single touch command.
You need to provide the file name as argument and not via standard input. You can use command substitution via $(…) or `…`:
while read line
do
touch "$(echo -e "$correctFilePathAndName")"
done < $file.txt
Ehm, lose the echo part... and use the correct variable name.
while read line; do
touch "$line"
done < $file.txt
try :
echo -e "$correctFilePathAndName" | touch
EDIT : Sorry correct piping is :
echo -e "$correctFilePathAndName" | xargs touch
The '<' redirects via stdin whereas touch needs the filename as an argument. xargs transforms stdin in an argument for touch.
I have need to execute a command in a script an arbitrary number of times with associated arbitrary parameters.
I've decided the script will take its cue from a parameter file (parameter.txt) where lines are of the form:
label param1 param2
For each line in parameter.txt, I'll call the command with the specified parameters.
So far, my tinkering is moving along the lines of the following, but it's looking messy:
while read line; do
echo $line | sed -r 's/[^ ]+ ([^ ]+).+/\1/' &&
echo $line | sed -r 's/[^ ]+ [^ ]+ ([^ ]+)/\1/'
done < parameter.txt
My command is of the form:
mycmd -a param1 -b param2 > label
Could I get some suggestions how I might simplify this?
I'm doing this for a small embedded system whose 'helper' commands are in short supply (xargs for example isn't available, and things like awk are hobbled busybox implementations), and I'm using version 2 (2.04g I think) of BASH.
while read label param1 param2; do
mycmd -a "$param1" -b "$param2" > "$label"
done < parameter.txt
I'd suggest a function, as long as there aren't any embedded spaces.
function x()
{
mycmd -a $2 -b $3 >$1
}
while read line; do x $line ; done <parameter.txt
Try this:
while read line ; do
set -- $line
dest="$1"
shift
mycmd "$#" > "$dest"
done < parameter.txt
should work. If the parameters in the file have spaces, you will have to quote them properly.
I suggest to add the -a, -b to the file parameter.txt because generating them on the fly is probably brittle.
If you don't like this solution, then I suggest to create a new script from this one which contains the actual commands. That way, you can easily debug any problems.
When the script looks okay, you can source it with source ./generated.sh (yes, you have to specify the path).
How do I iterate through each line of a text file with Bash?
With this script:
echo "Start!"
for p in (peptides.txt)
do
echo "${p}"
done
I get this output on the screen:
Start!
./runPep.sh: line 3: syntax error near unexpected token `('
./runPep.sh: line 3: `for p in (peptides.txt)'
(Later I want to do something more complicated with $p than just output to the screen.)
The environment variable SHELL is (from env):
SHELL=/bin/bash
/bin/bash --version output:
GNU bash, version 3.1.17(1)-release (x86_64-suse-linux-gnu)
Copyright (C) 2005 Free Software Foundation, Inc.
cat /proc/version output:
Linux version 2.6.18.2-34-default (geeko#buildhost) (gcc version 4.1.2 20061115 (prerelease) (SUSE Linux)) #1 SMP Mon Nov 27 11:46:27 UTC 2006
The file peptides.txt contains:
RKEKNVQ
IPKKLLQK
QYFHQLEKMNVK
IPKKLLQK
GDLSTALEVAIDCYEK
QYFHQLEKMNVKIPENIYR
RKEKNVQ
VLAKHGKLQDAIN
ILGFMK
LEDVALQILL
One way to do it is:
while read p; do
echo "$p"
done <peptides.txt
As pointed out in the comments, this has the side effects of trimming leading whitespace, interpreting backslash sequences, and skipping the last line if it's missing a terminating linefeed. If these are concerns, you can do:
while IFS="" read -r p || [ -n "$p" ]
do
printf '%s\n' "$p"
done < peptides.txt
Exceptionally, if the loop body may read from standard input, you can open the file using a different file descriptor:
while read -u 10 p; do
...
done 10<peptides.txt
Here, 10 is just an arbitrary number (different from 0, 1, 2).
cat peptides.txt | while read line
do
# do something with $line here
done
and the one-liner variant:
cat peptides.txt | while read line; do something_with_$line_here; done
These options will skip the last line of the file if there is no trailing line feed.
You can avoid this by the following:
cat peptides.txt | while read line || [[ -n $line ]];
do
# do something with $line here
done
Option 1a: While loop: Single line at a time: Input redirection
#!/bin/bash
filename='peptides.txt'
echo Start
while read p; do
echo "$p"
done < "$filename"
Option 1b: While loop: Single line at a time:
Open the file, read from a file descriptor (in this case file descriptor #4).
#!/bin/bash
filename='peptides.txt'
exec 4<"$filename"
echo Start
while read -u4 p ; do
echo "$p"
done
This is no better than other answers, but is one more way to get the job done in a file without spaces (see comments). I find that I often need one-liners to dig through lists in text files without the extra step of using separate script files.
for word in $(cat peptides.txt); do echo $word; done
This format allows me to put it all in one command-line. Change the "echo $word" portion to whatever you want and you can issue multiple commands separated by semicolons. The following example uses the file's contents as arguments into two other scripts you may have written.
for word in $(cat peptides.txt); do cmd_a.sh $word; cmd_b.py $word; done
Or if you intend to use this like a stream editor (learn sed) you can dump the output to another file as follows.
for word in $(cat peptides.txt); do cmd_a.sh $word; cmd_b.py $word; done > outfile.txt
I've used these as written above because I have used text files where I've created them with one word per line. (See comments) If you have spaces that you don't want splitting your words/lines, it gets a little uglier, but the same command still works as follows:
OLDIFS=$IFS; IFS=$'\n'; for line in $(cat peptides.txt); do cmd_a.sh $line; cmd_b.py $line; done > outfile.txt; IFS=$OLDIFS
This just tells the shell to split on newlines only, not spaces, then returns the environment back to what it was previously. At this point, you may want to consider putting it all into a shell script rather than squeezing it all into a single line, though.
Best of luck!
A few more things not covered by other answers:
Reading from a delimited file
# ':' is the delimiter here, and there are three fields on each line in the file
# IFS set below is restricted to the context of `read`, it doesn't affect any other code
while IFS=: read -r field1 field2 field3; do
# process the fields
# if the line has less than three fields, the missing fields will be set to an empty string
# if the line has more than three fields, `field3` will get all the values, including the third field plus the delimiter(s)
done < input.txt
Reading from the output of another command, using process substitution
while read -r line; do
# process the line
done < <(command ...)
This approach is better than command ... | while read -r line; do ... because the while loop here runs in the current shell rather than a subshell as in the case of the latter. See the related post A variable modified inside a while loop is not remembered.
Reading from a null delimited input, for example find ... -print0
while read -r -d '' line; do
# logic
# use a second 'read ... <<< "$line"' if we need to tokenize the line
done < <(find /path/to/dir -print0)
Related read: BashFAQ/020 - How can I find and safely handle file names containing newlines, spaces or both?
Reading from more than one file at a time
while read -u 3 -r line1 && read -u 4 -r line2; do
# process the lines
# note that the loop will end when we reach EOF on either of the files, because of the `&&`
done 3< input1.txt 4< input2.txt
Based on #chepner's answer here:
-u is a bash extension. For POSIX compatibility, each call would look something like read -r X <&3.
Reading a whole file into an array (Bash versions earlier to 4)
while read -r line; do
my_array+=("$line")
done < my_file
If the file ends with an incomplete line (newline missing at the end), then:
while read -r line || [[ $line ]]; do
my_array+=("$line")
done < my_file
Reading a whole file into an array (Bash versions 4x and later)
readarray -t my_array < my_file
or
mapfile -t my_array < my_file
And then
for line in "${my_array[#]}"; do
# process the lines
done
More about the shell builtins read and readarray commands - GNU
More about IFS - Wikipedia
BashFAQ/001 - How can I read a file (data stream, variable) line-by-line (and/or field-by-field)?
Related posts:
Creating an array from a text file in Bash
What is the difference between thee approaches to reading a file that has just one line?
Bash while read loop extremely slow compared to cat, why?
Use a while loop, like this:
while IFS= read -r line; do
echo "$line"
done <file
Notes:
If you don't set the IFS properly, you will lose indentation.
You should almost always use the -r option with read.
Don't read lines with for
If you don't want your read to be broken by newline character, use -
#!/bin/bash
while IFS='' read -r line || [[ -n "$line" ]]; do
echo "$line"
done < "$1"
Then run the script with file name as parameter.
Suppose you have this file:
$ cat /tmp/test.txt
Line 1
Line 2 has leading space
Line 3 followed by blank line
Line 5 (follows a blank line) and has trailing space
Line 6 has no ending CR
There are four elements that will alter the meaning of the file output read by many Bash solutions:
The blank line 4;
Leading or trailing spaces on two lines;
Maintaining the meaning of individual lines (i.e., each line is a record);
The line 6 not terminated with a CR.
If you want the text file line by line including blank lines and terminating lines without CR, you must use a while loop and you must have an alternate test for the final line.
Here are the methods that may change the file (in comparison to what cat returns):
1) Lose the last line and leading and trailing spaces:
$ while read -r p; do printf "%s\n" "'$p'"; done </tmp/test.txt
'Line 1'
'Line 2 has leading space'
'Line 3 followed by blank line'
''
'Line 5 (follows a blank line) and has trailing space'
(If you do while IFS= read -r p; do printf "%s\n" "'$p'"; done </tmp/test.txt instead, you preserve the leading and trailing spaces but still lose the last line if it is not terminated with CR)
2) Using process substitution with cat will reads the entire file in one gulp and loses the meaning of individual lines:
$ for p in "$(cat /tmp/test.txt)"; do printf "%s\n" "'$p'"; done
'Line 1
Line 2 has leading space
Line 3 followed by blank line
Line 5 (follows a blank line) and has trailing space
Line 6 has no ending CR'
(If you remove the " from $(cat /tmp/test.txt) you read the file word by word rather than one gulp. Also probably not what is intended...)
The most robust and simplest way to read a file line-by-line and preserve all spacing is:
$ while IFS= read -r line || [[ -n $line ]]; do printf "'%s'\n" "$line"; done </tmp/test.txt
'Line 1'
' Line 2 has leading space'
'Line 3 followed by blank line'
''
'Line 5 (follows a blank line) and has trailing space '
'Line 6 has no ending CR'
If you want to strip leading and trading spaces, remove the IFS= part:
$ while read -r line || [[ -n $line ]]; do printf "'%s'\n" "$line"; done </tmp/test.txt
'Line 1'
'Line 2 has leading space'
'Line 3 followed by blank line'
''
'Line 5 (follows a blank line) and has trailing space'
'Line 6 has no ending CR'
(A text file without a terminating \n, while fairly common, is considered broken under POSIX. If you can count on the trailing \n you do not need || [[ -n $line ]] in the while loop.)
More at the BASH FAQ
I like to use xargs instead of while. xargs is powerful and command line friendly
cat peptides.txt | xargs -I % sh -c "echo %"
With xargs, you can also add verbosity with -t and validation with -p
This might be the simplest answer and maybe it don't work in all cases, but it is working great for me:
while read line;do echo "$line";done<peptides.txt
if you need to enclose in parenthesis for spaces:
while read line;do echo \"$line\";done<peptides.txt
Ahhh this is pretty much the same as the answer that got upvoted most, but its all on one line.
#!/bin/bash
#
# Change the file name from "test" to desired input file
# (The comments in bash are prefixed with #'s)
for x in $(cat test.txt)
do
echo $x
done
Here is my real life example how to loop lines of another program output, check for substrings, drop double quotes from variable, use that variable outside of the loop. I guess quite many is asking these questions sooner or later.
##Parse FPS from first video stream, drop quotes from fps variable
## streams.stream.0.codec_type="video"
## streams.stream.0.r_frame_rate="24000/1001"
## streams.stream.0.avg_frame_rate="24000/1001"
FPS=unknown
while read -r line; do
if [[ $FPS == "unknown" ]] && [[ $line == *".codec_type=\"video\""* ]]; then
echo ParseFPS $line
FPS=parse
fi
if [[ $FPS == "parse" ]] && [[ $line == *".r_frame_rate="* ]]; then
echo ParseFPS $line
FPS=${line##*=}
FPS="${FPS%\"}"
FPS="${FPS#\"}"
fi
done <<< "$(ffprobe -v quiet -print_format flat -show_format -show_streams -i "$input")"
if [ "$FPS" == "unknown" ] || [ "$FPS" == "parse" ]; then
echo ParseFPS Unknown frame rate
fi
echo Found $FPS
Declare variable outside of the loop, set value and use it outside of loop requires done <<< "$(...)" syntax. Application need to be run within a context of current console. Quotes around the command keeps newlines of output stream.
Loop match for substrings then reads name=value pair, splits right-side part of last = character, drops first quote, drops last quote, we have a clean value to be used elsewhere.
This is coming rather very late, but with the thought that it may help someone, i am adding the answer. Also this may not be the best way. head command can be used with -n argument to read n lines from start of file and likewise tail command can be used to read from bottom. Now, to fetch nth line from file, we head n lines, pipe the data to tail only 1 line from the piped data.
TOTAL_LINES=`wc -l $USER_FILE | cut -d " " -f1 `
echo $TOTAL_LINES # To validate total lines in the file
for (( i=1 ; i <= $TOTAL_LINES; i++ ))
do
LINE=`head -n$i $USER_FILE | tail -n1`
echo $LINE
done
#Peter: This could work out for you-
echo "Start!";for p in $(cat ./pep); do
echo $p
done
This would return the output-
Start!
RKEKNVQ
IPKKLLQK
QYFHQLEKMNVK
IPKKLLQK
GDLSTALEVAIDCYEK
QYFHQLEKMNVKIPENIYR
RKEKNVQ
VLAKHGKLQDAIN
ILGFMK
LEDVALQILL
Another way to go about using xargs
<file_name | xargs -I {} echo {}
echo can be replaced with other commands or piped further.
for p in `cat peptides.txt`
do
echo "${p}"
done