I have many files in mypath that look like file_01.gz, file_02.gz, etc
I would like to compute the md5 checksums for each of them, and store the output in a text file with something like
filename md5
file01 fjiroeghreio
Is that possible on linux?
Many thanks!
md5sum file*.gz > output.txt
Output file is space separated, without header
You can use the shell filename expansion:
md5sum *.gz > file
Linux already has a tool called md5sum, so all you need to do is call it for every file you want. In the approach below you get the default format of the md5sum tool, "SUM NAME", one per line for each file found. By using the double redirect (>>) each call will append to the bottom of the output file, sums.txt
#!/bin/bash
for f in *.gz; do
md5sum "$f" >> sums.txt
done
The above is illustrative only, you should probably check for the pre-existence of the output file, deal with errors etc.
There's lots of ways of doing this, so it all depends on further requirements. Must the format be of the form you state, must it recurse directories etc.?
Related
I have read most questions regarding this topic, but can't get an answer to my specific question:
I have a number of files in a directory, and I want to apply a command to each of these files and then create a new file with the outpot for every single file. I can only manage to write it into one file alltogether. As i expect to have ~ 500.000 files, i also would need the script to be as efficient as possible.
for f in *.bed; do sort -k1,1 -k2,2n; done
This command sorts each file accordingly and writes the ouput in the Shell - But i cannot manage to write to file in the for-loop without appending it with ">>" .
I'm thankful for any answer providing an approach or an already answered question on this topic!
You can use script like this:
for f in *.bed
do
sort -k1,1 -k2,2n $f >>new_filename
done
If you want to be sure new_filename is empty before run the loop you can clear the content in file with command (before for loop):
>new_filename
So, I want to insert test in .txt but when I try
type file1.txt >> file2.txt
and sort it using cygwin with sort file1 | uniq >> sorted it will place it at the end of the file. But i want to write it to the start of the file. I don't know if this is possible in cmd and if it's not I can also do it in a linux terminal.
Is there a special flag or operator I need to use?
Thanks in regards, Davin
edit: the file itself (the file i'm writing to) is about 5GB big so i would have to write 5GB to a file every time i wanted to change anything
It is not possible to write to the start of the file. You can only replace the file content with content provided or append to the end of a file. So if you need to add the sorted output in front of the sorted file, you have to do it like that:
mv sorted sorted.old
sort file1 | uniq > sorted
cat sorted.old >> sorted
rm sorted.old
This is not a limitation of the shell but of the file APIs of pretty much every existing operating system. The size of a file can only be changed at the end, so you can increase it, in that case the file will grow at the end (all content stays as it is but now there is empty space after the content) or you can truncate it (in that case content is cut off at the end). It is possible to copy data around within a file but there exists no system function to do that, you have to do it yourself and this is almost as inefficient as the solution shown above.
I was generating a sequence of png images in my program, which files I was planning to get is passed through some tool that converts them to a video file. I am generating files one by one, in the proper sequence that I want them. I want to name them in such a way that the subsequent video conversion tool will take them in proper sequence under the file name globbing used by the shell ( I am using bash with Linux.). I tried adding a numeric sequence like 'scene1.png, scene10.png, scene12.png, but the shell doesn't sort globs numerically. I could pass a sorted list like this:
convert -antialias -delay 1x10 $(ls povs/*.png | sort -V) mymovie.mp4
But some programs do their own globbing and don't use shells globbing ( like FFmpeg), and so this approach does not always work. so I am looking for a scheme of naming files that are guaranteed to be in sequence as per shell globbing rules.
You may prefix your files with a zero padded integer.
This script emulates what ls * should output after renaming :
$ for i in {1..12};do
$ printf '%05d_%s\n' ${i} file${i}
$ done;
00000_file0
00001_file1
00002_file2
00003_file3
00004_file4
00005_file5
00006_file6
00007_file7
00008_file8
00009_file9
00010_file10
00011_file11
I have multiple .tsv files named as choochoo1.tsv, choochoo2.tsv, ... choochoo(nth).tsv files. I also have a main.tsv file. I want to extract the header line in main.tsv and paste over all choochoo(nth).tsv files. Please note that there are other .tsv files in the directory that I don't want to change or paste header, so I can't do *.tsv and select all the .tsv files (so need to select choochoo string for wanted files). This is what I have tried using bash script, but could not make it work. Please suggest the right way to do it.
for x in *choochoo; do
head -n1 main.tsv > $x
done
You have a problem with the file glob, as well as the redirect:
the file glob will catch things like AAchoochoo but not choochoo1.tsv and not even AAchoochoo.tsv
the redirect will overwrite the existing files instead of adding to them. The redirect command for adding to a file is >>, but that will append text to the end and you want to prepend text in the beginning.
The problem with prepending text to an existing file, is that you have to open the file for both reading and writing and then stream both prepended text and original text, in order - and that is usually where people fail because the shell can't open files like that (there is a slightly more complex way of doing this directly, by opening the file for both reading and writing, but I'm not going to address that further).
You might want to use a temporary file, something like this:
for x in choochoo[0-9]*.tsv; do
mv "$x"{,.orig}
(head -n1 main.tsv; cat "$x.orig") > $x
rm "$x.orig"
done
When we use the redirect IO operator for a shell script does the operator keep all the data to be written in memory and write it all at once or does write it to file line by line.
Here is what i am working on.
I have about 200 small files ~1000 lines each in a specific format. I want to process (do a regex and change the format a little) each line in all the files and have the new transformed lines in a single combined file.
I have a transformscript.sh that takes a single file and applies the transformation. I run it in the following manner
sh transformscript.sh somefile.txt > newfile.txt
This works fine and fast for a single file.
How do i extend to do it for all the files. will it be efficient to change transformscript.sh to take a directory as argument instead of filename and add a for loop to transform all the lines of all the files together. Or should I run the above trnsformscript.sh for each file and create a new file for each one and combine then separately.
Thanks.
The redirect operator simply opens the file for writing and passes that file descriptor to the shell as its standard output. The shell then writes to the file directly.
You probably do NOT want to run the script separately for each file since you will incur the overhead of bash process creation for each pass. For example:
# don't do it this way
for somefile in $(ls somefiles*.txt); do
newfile=${somefile//some/new}
sh transformscript.sh $somefile > $newfile
done
The above starts one shell for every file found which is pretty inefficient. It would be better to rewrite transformscript.sh to handle multiple files if possible. Depending on how complicated your transform is and whether you need to keep the original filenames, you might be able to use a single sed process. For example, assume you have 200 files named test1.txt through test200.txt all with a "Hello world" line you want to change to "Hello joe". You could do something as simple a this:
sed -i.save 's/Hello world/Hello joe/' test*.txt
The -i tells sed to do an "in place" edit (edit the original file) and the optional ".save" argument to -i makes a backup copy of the original file with a .save extension before editing the original file. Note, this will leave the original contents in the .save files and the new content in the files with the original name which may not be what you want.