My input file's contents are:
welcome
welcome1
welcome2
My script is:
for groupline in `cat file`
do
echo $groupline;
done
I got the following output:
welcome
welcome1
welcome2
Why doesn't it print the empty line?
you need to set IFS to newline \n
IFS=$"\n"
for groupline in $(cat file)
do
echo "$groupline";
done
Or put double quotes. See here for explanation
for groupline in "$(cat file)"
do
echo "$groupline";
done
without meddling with IFS, the "proper" way is to use while read loop
while read -r line
do
echo "$line"
done <"file"
Because you're doing it all wrong. You want while not for, and you want read, not cat:
while read groupline
do
echo "$groupline"
done < file
The solution ghostdog74 provided is helpful, but has a flaw.
IFS could not use double quotes (at least in Mac OS X), but can use single quotes like:
IFS=$'\n'
It's nice but not dash-compatible, maybe this is better:
IFS='
'
The blank line will be eaten in the following program:
IFS='
'
for line in $(cat file)
do
echo "$line"
done
But you can not add double quotes around $(cat file), it will treat the whole file as one single string.
for line in "$(cat file)"
If want blank line also be processed, using the following
while read line
do
echo "$line"
done < file
Using IFS=$"\n" and var=$(cat text.txt) removes all the "n" characters from the output echo $var
Related
I'm reading some file paths and names from a text file and trying to test if file exists. I'm not sure what I'm doing wrong but first echo returns filepath and file name whilst the echo inside the if statement doesn't. Any ideas?
#!/bin/bash
while read line; do
echo $line
if [ -f "$line" ]; then
echo "found: $line"
fi
done < /mbackup/temp/images.txt
The only change is adding the -r option to read. That option is documented as:
Backslash does not act as an escape character. The backslash is considered to be part of the line. In particular, a backslash-newline pair may not then be used as a line continuation.
This helps prevent special characters in file names from interfering with your script.
I test this with files containing special characters and it works as you expected.
#!/bin/bash
while read -r line; do
echo $line
if [ -f "$line" ]; then
echo "found: $line"
fi
done < /mbackup/temp/images.txt
How do I iterate through each line of a text file with Bash?
With this script:
echo "Start!"
for p in (peptides.txt)
do
echo "${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
I'm having an issue in something that seems to be a rookie error, but I can't find a way to find a solution.
I have a bash script : log.sh
which is :
#!/bin/bash
echo $1 >> log_out.txt
And with a file made of filenames (taken from the output of "find" which names is filesnames.txt and contains 53 lines of absolute paths) I try :
./log.sh $(cat filenames.txt)
the only output I have in the log_out.txt is the first line.
I need each line to be processed separately as I need to put them in arguments in a pipeline with 2 softwares.
I checked for :
my lines being terminated with /n
using a simple echo without writing to a file
all the sorts of cat filenames.txt or (< filenames.txt) found on internet
I'm sure it's a very dumb thing, but I can't find why I can't iterate more than one line :(
Thanks
It is because your ./log.sh $(cat filenames.txt) is being treated as one argument.
while IFS= read -r line; do
echo "$line";
done < filenames.txt
Edit according to: https://mywiki.wooledge.org/DontReadLinesWithFor
Edit#2:
To preserve leading and trailing whitespace in the result, set IFS to the null string.
You could simplify more and skip using explicit variable and use the default $REPLY
Source: http://wiki.bash-hackers.org/commands/builtin/read
You need to quote the command substitution. Otherwise $1 will just be the first word in the file.
./log.sh "$(cat filenames.txt)"
You should also quote the variable in the script, otherwise all the newlines will be converted to spaces.
echo "$1" >> log_out.txt
If you want to process each word separately, you can leave out the quotes
./log.sh $(cat filenames.txt)
and then use a loop in the script:
#!/bin/bash
for word in "$#"
do
echo "$word"
done >> log_out.txt
Note that this solution only works correctly when the file has one word per line and there are no wildcards in the words. See mywiki.wooledge.org/DontReadLinesWithFor for why this doesn't generalize to more complex lines.
You can iterate with each line.
#!/bin/bash
for i in $*
do
echo $i >> log_out.txt
done
How do I iterate through each line of a text file with Bash?
With this script:
echo "Start!"
for p in (peptides.txt)
do
echo "${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
in shell scripts I usually append a string to variable with "${variable} end". However, I have a file "file.txt" in which I want all lines to be appended by "end". So command line I do, for instance, for i in `cat file.txt`; do echo "${i} end"; done. But the word "end" (pluse the space) will not be appended but appended. The same thing happends when I use a while loop. Could anybody tell me what is going on right there? I am using GNU bash version 4.2.37 on LinuxMint13 64bit (both Cinammon and Mate).
Thank you for any help!
You should use a while loop instead of a for loop, as explained here.
while IFS= read -r line
do
echo "$line end"
done < "file.txt"
It may just be your syntax - don't forget do. That is:
for i in `cat file.txt`; do echo "${i} end"; done
If you're asking how to make a new file with "end" appended to each line, try this:
for i in `cat file.txt`; do echo "${i} end" >> some_new_file; done
Is using a loop the only option? If all you want to do is append something to the end of every line, it's probably easier to use sed:
sed -ie 's/.*/& end/' file.txt