Open mihkelvaher opened 3 years ago
Hi!
Sure, that's something that can be done. I'm in the process of adding an option -o
to sketch that can take '/dev/stdout' or '-', which I'll probably finish later today. (The option is there, but it is currently broken.)
Thanks,
Daniel
That's great! Also, can smaller sketches be compared with larger ones? For example, if I have some bacteria and human in the same database, do I need to scale up the bacterial sketches if I don't want to lose too much human info?
Hi Mihkel --
They can't be compared directly, but you can compress larger sketches by folding them in half repeatedly, if you will. I've added a new subcommand dashing fold
which should compress a larger HLL into a smaller sketch.
The above issue about directing sketch output to a stream has been fixed, and once the new binaries finish compiling they should be ready to use. I'll let you know when it's avaiable.
Thanks,
Daniel
Hi Daniel,
The pull request suggested that the option is now available on main.
Unfortunately, I don't know how to use it and -o
isn't listed in dashing sketch -h
.
What I tried (and similar):
cat test.fasta | dashing sketch - -o test.sketch
Sketching the old way, I gave fold
also a try but
[src/main.cpp:int main(int, char**)56] Invalid subcommand fold provided.
I'm guessing I've got a wrong version (v0.5-9-ge6ae
), but the pull request was also merged to main/master...
Thanks.
Is it possible to create a sketch using fastas streamed through a pipe to dashing?
I'm manipulating both assembled genomes and k-mers and would like to compare them in the end multiple times. I could write them on the disk as an additional step but given the high volume, it is really cumbersome.
Thanks.