Providing context helps us come up with a solution and improve our documentation for the future.
The help for modules that use --taxon-list allows for comma separated values:
--taxon-list STR Taxonomy ID, possibly multiple values separated by ',' []
Your Environment
Include as many relevant details about the environment you experienced the bug in.
Git commit used (The string after "MMseqs Version:" when you execute MMseqs without any parameters): e2510e8f6911e4340c62989aa9ba1b9c58e18d60
Which MMseqs version was used (Statically-compiled, self-compiled, Homebrew, etc.): self-compiled
For self-compiled and Homebrew: Compiler and Cmake versions used and their invocation: cmake version 3.5.1, c++ (Ubuntu 5.4.0-6ubuntu1~16.04.12) 5.4.0 20160609
Server specifications (especially CPU support for AVX2/SSE and amount of system memory):
MMseqs2 does something more sensible with , in --taxon-list. No idea what to do about the validation step though. We could add a regex to check for only sensible operators and numbers?
Expected Behavior
Expected the following two commands to result in the same database:
mmseqs filtertaxseqdb swissProtSomeClasses test1 --taxon-list '4891||1075807||147549'
and
mmseqs filtertaxseqdb swissProtSomeClasses test2 --taxon-list '4891,1075807,147549'
Also expected the following command to fail/throw warning:
mmseqs filtertaxseqdb swissProtSomeClasses test3 --taxon-list '489!@!@1075807****147549'
Current Behavior
The first two commands result in two different databases:
wc -l test1
15447 test1wc -l test2
32 test2The third command runs without issuing any warning (it effectively does nothing to the database).
Steps to Reproduce (for bugs)
Please make sure to execute the reproduction steps with newly recreated and empty tmp folders.
MMseqs Output (for bugs)
Please make sure to also post the complete output of MMseqs. You can use gist.github.com for large output.
and
Context
Providing context helps us come up with a solution and improve our documentation for the future.
The help for modules that use
--taxon-list
allows for comma separated values:--taxon-list STR Taxonomy ID, possibly multiple values separated by ',' []
Your Environment
Include as many relevant details about the environment you experienced the bug in.