While I still write a decent amount of shell I generally try to avoid
it. It’s hard for others to read, has a lot of sharp edges, tends to
swallow errors, and handles the unusual situations poorly. But one
thing that keeps me coming back to it is how easily I can set up trees
of processes.
Say I have a program that reads two files together in a single pass
[1] and writes something out. The inputs you have are compressed, so
you’ll need to decompress them, and the output needs to be compressed
before you write it out to storage. You could do:
# download the files
aws s3 cp “$path1” .
aws s3 cp “$path2″ .
# decompress the files
gunzip “$file1”
gunzip “$file2″
# run the command
cmd −1 “$file1” −2 “$file2″ > “$fileOut”
# compress the output
gzip “$fileOut”
# upload the output
aws s3 cp “$fileOut.gz” “$pathOut”
This works, but for large files it’s slow and needs too much space.
We’re waiting for each step to finish before starting the next, and
we’re storing some very large intermediate files on the local
machine.
Instead, we’d like to stream the inputs down, decompress them as we
go, compress the output as it comes out, and stream the output back
up. In bash this is reasonably straightforward to write:
This uses almost no disk space and it parallelizes the decompression,
command, and recompression. But it’s also shell…
I tend to use python for this kind of thing, where I’m gluing things
together and want it to be clear what I’m doing. It seems like it
should be possible to do this sort of thing with the subprocess
module, but while I’ve played with it a few times I haven’t figured it
out. I’d like an API like:
These are 5x and 3x the length of the bash version, but I’d be willing
to put up with that for having something that’s more robust. The
difference would also be smaller in practice as the commands would
typically have a lot of arguments.
I see these
stackoverflow
answers suggesting named pipes, but they seem awkward, hard to
read, and easy to get wrong. Is there a better way? Should I just
stick with bash when doing something bash is this good a fit for,
especially now that people can paste my code into an LLM and get an
explanation of what it’s doing?
[1] Interleaved fastq files, where the Nth record in file 1
corresponds to the Nth record in file 2.
Process Substitution Without Shell?
Link post
While I still write a decent amount of shell I generally try to avoid it. It’s hard for others to read, has a lot of sharp edges, tends to swallow errors, and handles the unusual situations poorly. But one thing that keeps me coming back to it is how easily I can set up trees of processes.
Say I have a program that reads two files together in a single pass [1] and writes something out. The inputs you have are compressed, so you’ll need to decompress them, and the output needs to be compressed before you write it out to storage. You could do:
This works, but for large files it’s slow and needs too much space. We’re waiting for each step to finish before starting the next, and we’re storing some very large intermediate files on the local machine.
Instead, we’d like to stream the inputs down, decompress them as we go, compress the output as it comes out, and stream the output back up. In bash this is reasonably straightforward to write:
This uses almost no disk space and it parallelizes the decompression, command, and recompression. But it’s also shell…
I tend to use python for this kind of thing, where I’m gluing things together and want it to be clear what I’m doing. It seems like it should be possible to do this sort of thing with the subprocess module, but while I’ve played with it a few times I haven’t figured it out. I’d like an API like:
Or:
These are 5x and 3x the length of the bash version, but I’d be willing to put up with that for having something that’s more robust. The difference would also be smaller in practice as the commands would typically have a lot of arguments.
I see these stack overflow answers suggesting named pipes, but they seem awkward, hard to read, and easy to get wrong. Is there a better way? Should I just stick with bash when doing something bash is this good a fit for, especially now that people can paste my code into an LLM and get an explanation of what it’s doing?
[1] Interleaved
fastq
files, where the Nth record in file 1 corresponds to the Nth record in file 2.