On my MacBook Pro, I'm trying to delete two ranges from multiple files in a directory. Searching thus far, it seems like sed is a way to do it, but if I try to delete one of the ranges with the command:
sed -i '5825,6144d' *.tab.txt
I get the error message:
sed: 1: "cl9_408230953ref_f00507 ...": command c expects \ followed by text
Alternatively, I've tried other variants where the command seems to work (i.e., no error message), but the files haven't changed. Suggestions?
Use
sed -i '' '5825,6144d' *.tab.txt
Or
sed -i.bak '5825,6144d' *.tab.txt
Related
sed -i s/CUSTOMER_UNIT=".*"/CUSTOMER_UNIT="Test" core/src/main/java/com/appname/core/AppConstants.kt
I am running this sed command as a result I get this
sed: ore/src/main/java/com/appname/core/AppConstants.kt: No such file or directory
It remove the first letter of core -> ore
but if I just run command find ore/src/main/java/com/appname/core/AppConstants.kt it this file exists
I am not sure if you are trying to have the results = core or ore
but when i replicate I am able to get core. One thing I noticed is in your example you are missing the terminating / for your sed command after "Test"
sed -i s/CUSTOMER_UNIT=".*"/CUSTOMER_UNIT="Test"/ core/src/main/java/com/appname/core/AppConstants.kt
sed: can't read core/src/main/java/com/appname/core/AppConstants.kt: No such file or directory
if you are trying to cut the C from core and you can manually validate the path exists I would be sure that you have proper permissions
The command should be enclosed in quotes and be ended with "/".
sed -i 's/CUSTOMER_UNIT=".*"/CUSTOMER_UNIT="Test"/' core/src/main/java/com/appname/core/AppConstants.kt
I'm using the commands given below for splitting my fastq file into two separate paired end reads files:
grep '#.*/1' -A 3 24538_7#2.fq >24538_7#2_1.fq
grep '#.*/2' -A 3 24538_7#2.fq >24538_7#2_2.fq
But it's automatically introducing a -- line separator between the entries. Hence, making my fastq file inappropriate for further processing(because it then becomes an invalid fastq format).
So, I want to get rid of the line separator(--).
PS: I've found the answer for Linux machine but I'm using MacOS, and those didn't work on Mac terminal.
You can use the --no-group-separator option to suppress it (in GNU grep).
Alternatively, you could use (GNU) sed:
sed '\|#.*/1|,+3!d'
deletes all lines other than the one matching #.*/1 and the next three lines.
For macOS sed, you could use
sed -n '\|#.*/1|{N;N;N;p;}'
but this gets unwieldy quickly for more context lines.
Another approach would be to chain grep with itself:
grep '#.*/1' -A 3 file.fq | grep -v "^--"
The second grep selects non-matching (-v) lines that start with -- (though this pattern can sometimes be interpreted as a command line option, requiring some weird escaping like "[-][-]", which is why i put the ^ there).
I'm attempting to remove a line from several hundred files. The following does exactly what I need but, it doesn't save changes (as expected).
$ grep -v meow src/files
I've seen that appending > to the end of a given command will specify where the output buffer should save but, does this work for multiple files?
So I'd like to know if there's an elegant way to mass edit via the terminal. All of the examples I've come across using awk or sed only provide solutions for editing one file at a time.
One way to do this is using the following Perl one-liner:
perl -i.bak -n -e 'print unless /meow/' src/files
This should do in-place editing of multiple files. The originals are saved in .bak files.
Another way to do it is to do a similar operation with sed:
sed -i .bak '/meow/d' src/files/*
Perl got its -i option from sed, after all. Note that to use no backup file, you need an explicit empty extension with at least some versions of sed:
sed -i '' '/meow/d' src/files/*
On my Mac, when I try to run:
sed -i 2d file.csv
from the answer to Unix script to remove the first line of a CSV file, I get the following error:
sed: 1: "file.csv": invalid command code f
What can I do if I would like to delete the first two lines of file.csv?
On a Mac, the BSD sed requires the suffix for the backup (but the suffix can be an empty string, '') — it is not optional as it is with GNU sed. Hence, your command is being interpreted as "backup the file with the suffix 2d and … oops, the script you gave is file.csv, but f isn't a sed command".
sed -i .bak -e 2d file.csv
This deletes the first line of data from the CSV file (leaving the heading line in place).
If you want to write the code so it works with both BSD and GNU sed, then you have to attach the suffix to the -i option (GNU sed requires the suffix attached to the -i option; that's how it identifies whether there's an optional suffix or not):
sed -i.bak -e 2d file.csv
Note that you can't use an empty suffix and have the command work with both BSD sed and GNU sed.
The -e isn't necessary in either command line, but I quite often use it. I also often quote the command in single quotes, though it isn't necessary here.
If you want to delete the first two data lines, use 2,3d as the command. If you want to delete the first two lines, use 1,2d.
If you don't want the backup, then you can either remove it after the sed command completes (easiest) or use the two stage or three stage dance:
sed 2d file.csv > file.csv.bak &&
mv file.csv.bak file.csv # Oops; there went the links
sed 2d file.csv > file.csv.bak &&
cp file.csv.bak file.csv
rm -f file.csv.bak
With these, you might need to add trap commands to clean up the intermediate .bak file if an interrupt or other signal terminates the script.
To quote from the Apple documentation for sed — which was originally quoted by Diego in an answer which he chose to delete, the -i option takes an argument which indicates the extension to use for backup copies.
-i extension
Edit files in-place, saving backups with the specified extension. If a zero-length extension is given, no backup will be saved. It is not recommended to give a zero-length extension when in-place editing files, as you risk corruption or partial content in situations where disk space is exhausted, etc.
sed -i.bak '2,3d' filename.csv will delete lines 1 and 2 (assuming you have headers)
What this command does is edits the file being referenced while simultaneously creating a backup of the original file (hence the usage of .bak). The line deletion '2,3d' will delete the 2nd and 3rd line of the original file.
For some mysterious reason, some elements in my CSV data appear as s/stWgvN52??f2& ?" instead of stWgvN522tw0JtZZnyXj, which messes up the file because I have ; set as the CSV delimiter.
I attempted to replace the defective string using sed as follows:
$ sed -i 's/stWgvN52??f2& ?"/stWgvN522tw0JtZZnyXj/g' file.csv
but I get the following error:
sed: 1: "access_logs_2014-04.csv": command a expects \ followed by text
What is the reason?
When you use the -i option, you have to specify the extension of the backup file that gets made. Some versions of sed expect the extension directly appended to the -i option, so what you wrote would work. But other versions (like the version on OS X) require it to be a separate option, so you have to write:
sed -i '' 's/stWgvN52??f2& ?"/stWgvN522tw0JtZZnyXj/g' file.csv
to specify that you don't want a backup file.