I would like to rename many files in this format
abc.123.fits
abcd.1234.fits
efg.12.fits
to this format
abc.fits
abcd.fits
efg.fits
I tried the rename function, but since the part I'm trying to replace is not the same in all files, it did not work. I am using Linux.
for f in *; do mv "$f" "${f%%.*}.${f##*.}"; done`
${f%%.*} removes everything after the first period, including the period. ${f##*.} removes everything before the last period, including the period (i.e. it gets the file extension). Concatenating these two, with a period between them, gives you the desired result.
You can change the * to a more restrictive pattern such as *.fits if you don't want to rename all files in the current directory. The quotes around the parameters to mv are necessary if any filenames contain whitespace.
Many other variable substitution expressions are available in bash; see a reference such as TLDP's Bash Parameter Substitution for more information.
Related
I've got a ton of files as follows
audiofile_drums_1-ktpcwybsh5c.wav
soundsample_drums_2-fghlkjy57sa.wav
noise_snippet_guitar_5-mxjtgqta3o1.wav
louder_flute_9-mdlsiqpfj6c.wav
I want to remove everything between and including the "-" and the .wav file extension, to be left with
audiofile_drums_1.wav
soundsample_drums_2.wav
noise_snippet_guitar_5.wav
louder_flute_9.wav
I've tried to do delete everything following and including the character "-" using
rename 's/-.*//' *
Which gives me
audiofile_drums_1
soundsample_drums_2
noise_snippet_guitar_5
louder_flute_9
And for lack of finding an easy way to rename all the files again, adding .wav the extension, I am hoping there is a slicker way to do this in one nifty command in one stage instead of 2.
Any suggestions?
Thanks
You can use rename 's/-[^\.]*\.wav$/\.wav/' *
The first part -[^\.]*\.wav$ searchs for a - followed by n chars that are not . followed by .wav and the end of filename. The end of filename and .wav is not strictly needed but it helps avoid renaming files you don't want to rename.
The /\.wav/ preserves the extension.
Please not that rename is not a standard utility, and is part of perl, so rename may not be available on every linux system.
This works in my specific case, but should work for any file extension.
rename -n 's/-.*(?=\.wav$)//' *
The command looks for all characters after and inclusive of the - symbol in the filename, then, using a positive lookahead** (?=\.wav$) to search for the characters (the file extension in this case) at the end of the filename (denoted by $, and replaces them with no characters (removing them).
** NOTE: A positive look ahead is a zero width assertion.
It will affect the match but it will not be included
in the replacement. (The '.wav' part will not be
erased)
In this example (?=\.wav$) is the positive lookahead. The dollar sign $, as in regex, denotes at the end of the line, so perfect for a file extension.
I have a few thousand files named as follows:
Cyprinus_carpio_600_nanopore_trim_reads.fasta
Cyprinus_carpio_700_nanopore_trim_reads.fasta
Cyprinus_carpio_800_nanopore_trim_reads.fasta
Cyprinus_carpio_900_nanopore_trim_reads.fasta
Vibrio_cholerae_3900_nanopore_trim_reads.fasta
for 80 variations of the first two words (80 different species), i would like to rename all of these files such that the number is increased by 100 - for example:
Vibrio_cholerae_3900_nanopore_trim_reads.fasta
would become
Vibrio_cholerae_4000_nanopore_trim_reads.fasta
or
Cyprinus_carpio_300_nanopore_trim_reads.fasta
would become
Cyprinus_carpio_400_nanopore_trim_reads.fasta
Unfortunately I can't work out how to get to rename them, i've had some luck with following the solutions on https://unix.stackexchange.com/questions/40523/rename-files-by-incrementing-a-number-within-the-filename
But i can't get it to work for the inside of the name, i'm running on Ubuntu 18.04 if that helps
If you can get hold of the Perl-flavoured version of rename, that is simple like this:
rename -n 's/(\d+)/$1 + 100/e' *fasta
Sample Output
'Ciprianus_maximus_11_fred.fasta' would be renamed to 'Ciprianus_maximus_111_fred.fasta'
'Ciprianus_maximus_300_fred.fasta' would be renamed to 'Ciprianus_maximus_400_fred.fasta'
'Ciprianus_maximus_3900_fred.fasta' would be renamed to 'Ciprianus_maximus_4000_fred.fasta'
If you can't read Perl, that says... "Do a single substitution as follows. Wherever you see a bunch of digits next to each other in a row (\d+), remember them (because I put that in parentheses), and then replace them with the evaluated expression of that bunch of digits ($1) plus 100.".
Remove the -n if the dry-run looks correct. The only "tricky part" is the use of e at the end of the substitution which means evaluate the expression in the substitution - or I call it a "calculated replacement".
If there is only one number in your string then below two line of code should provide help you resolve your issue
filename="Vibrio_cholerae_3900_nanopore_trim_reads.fasta"
var=$(echo $filename | grep -oP '\d+')
echo ${filename/${var}/$((var+100))}
Instead of echoing the changed file name, you can take it into a variable and use mv command to rename it
Considering the filename conflicts in the increasing order, I first thought of reversing the order but there still remains the possibility of conflicts in the alphabetical (standard) sort due to the difference to the numerical sort.
Then how about a two-step solution: in the 1st step, an escape character (or whatever character which does not appear in the filename) is inserted in the filename and it is removed in the 2nd step.
#!/bin/bash
esc=$'\033' # ESC character
# 1st pass: increase the number by 100 and insert a ESC before it
for f in *.fasta; do
num=${f//[^0-9]/}
num2=$((num + 100))
f2=${f/$num/$esc$num2}
mv "$f" "$f2"
done
# 2nd pass: remove the ESC from the filename
for f in *.fasta; do
f2=${f/$esc/}
mv "$f" "$f2"
done
Mark's perl-rename solution looks great but you should apply it twice with a bump of 50 to avoid name conflict. If you can't find this flavor of rename you could try my rene.py (https://rene-file-renamer.sourceforge.io) for which the command would be (also applied twice) rene *_*_*_* *_*_?_* B/50. rene would be a little easier because it automatically shows you the changes and asks whether you want to make them and it has an undo if you change your mind.
I am copying some specific lines from one file to another.
grep '^stringmatch' /path/sfile-*.cfg >> /path/nfile-*.cfg
Here what's happening: its creating a new file called nfile-*.cfg and copying those lines in that. The file names sfile- * and nfile- * are randomly generated and are generally followed by a number. Both sfile-* and nfile-* are existing files and there is only one such file in the same directory. Only the number that follows is randomly generated. The numbers following in sfile and nfile need not be same. The files are not created simultaneously but are generated when a specific command is given. But some lines from one file to the another file needs to be appended.
I'm guessing you actually want something like
for f in /path/sfile-*.cfg; do
grep '^stringmatch' "$f" >"/path/nfile-${f#/path/sfile-}"
done
This will loop over all sfile matches and create an nfile target file with the same number after the dash as the corresponding source sfile. (The parameter substitution ${variable#prefix} returns the value of variable with any leading match on the pattern prefix removed.)
If there is only one matching file, the loop will only run once. If there are no matches on the wildcard, the loop will still run once unless you enable nullglob, which changes the shell's globbing behavior so that wildcards with no matches expand into nothing, instead of to the wildcard expression itself. If you don't want to enable nullglob, a common workaround is to add this inside the loop, before the grep;
test -e "$f" || break
If you want the loop to only process the first match if there are several, add break on a line by itself before the done.
If I interpret your question correctly, you want to output to an existing nfile, which has a random number in it, but instead the shell is creating a file with an asterisk in it, so literally nfile-*.cfg.
This is happening because the nfile doesn't exist when you first run the command. If the file doesn't exist, bash will fail to expand nfile-*.cfg and will instead use the * as a literal character. This is correct behaviour in bash.
So, it looks like the problem is that the nfile doesn't exist when you start your grep. You'll need to create one.
I'll leave code to others, but I hope the explanation is useful.
I have a folder that was created automatically. The user unintentionally provided smart (curly) quotes as part of the name, and the process that sanitizes the inputs did not catch these. As a result, the folder name contains the smart quotes. For example:
this-is-my-folder’s-name-“Bob”
I'm now trying to rename/remove said folder on the command line, and none of the standard tricks for dealing with files/folders with special characters (enclosing in quotes, escaping the characters, trying to rename it by inode, etc.) are working. All result in:
mv: cannot move this-is-my-folder’s-name-“Bob” to this-is-my-folders-name-BOB: No such file or directory
Can anyone provide some advice as to how I can achieve this?
To get the name in a format you can copy-and-paste into your shell:
printf '%q\n' this*
...will print out the filename in a manner the shell will accept as valid input. This might look something like:
$'this-is-my-folder200\231s-name-200\234Bob200\235'
...which you can then use as an argument to mv:
mv $'this-is-my-folder200\231s-name-200\234Bob200\235' this-is-my-folders-name-BOB
Incidentally, if your operating system works the same way mine does (when running the test above), this would explain why using single-character globs such as ? for those characters didn't work: They're actually more than one byte long each!
You can use shell globbing token ? to match any single character, so matching the smart quotes using ? should do:
mv this-is-my-folder?s-name-?Bob? new_name
Here replacing the smart quotes with ? to match the file name.
There are several possibilities.
If an initial substring of the file name ending before the first quote is unique within the directory, then you can use filename completion to help you type an appropriate command. Type "mv" (without the quotes) and the unique initial substring, then press the TAB key to request filename completion. Bash will complete the filename with the correct characters, correctly escaped.
Use a graphical file browser. Then you can select the file to rename by clicking on it. (Details of how to proceed from there depend on the browser.) If you don't have a graphical terminal and can't get one, then you may be able to do the same with a text-mode browser such as Midnight Commander.
A simple glob built with the ? or * wildcard should be able to match the filename
Use a more complex glob to select the filename, and perhaps others with the same problem. Maybe something like *[^a-zA-Z0-9-]* would do. Use a pattern substitution to assign a new name. Something like this:
for f in *[^a-zA-Z0-9-]*; do
mv "$f" "${f//[^a-zA-Z0-9-]/}"
done
The substitution replaces all appearances of a characters that are not decimal digits, appercase or lowercase Latin letters, or hyphens with nothing (i.e. it strips them). Do take care before you use this, though, to make sure you're not going to make more changes than you intend to do.
Alright, so I'm trying to combine some but not all of my script's parameters into one string. I'm trying to write a script that changes spaces in a file name to underscores, and when the option -r is given, it recursively does it to every file in the folder.
Assuming the file is saved as removespaces.sh, if you run removespaces.sh file with spaces.doc it doesn't really have to care about parameters, I can just use $*
but, when I'm trying to do it for an entire folder I now have -r as $1. So I can't just (be lazy) use $*.. how could I create a string that's equal to $2 to end?
A string of $2 to the end of the parameters:
"${*:2}"
This differs from "${#:2}" in that it concatenates all the arguments, with one space between each. In general, it is possible that neither form is what you want (if, for example, you have files with more than one consecutive space in their name).