I am using the taxonomy2function tool and would like to recover the function from a specific taxonomy level, (Family i.e.). There is the -ac, --firstClasses [string(s)] Class IDs in first classification?. Default value(s): ‘all’. parameter.
When I set this parameter to recovery “Domain” I received this error ----firstClasses : integer expected, got: Domain. I changed it to Integer 2, and now the tool works properly.
However, the output is empty when I try another integer, like 6.
Below is the command line:
taxonomy2function -i Pp2.fastq.blastx_NR.diamond.daa -a Taxonomy -b SEED -ac 6 -sh true -au false -bu false -o teste_tax2func
How can I select a specific taxonomy level using the “-ac” parameter?
The problem is that the -ac option expects a list of taxon (or class) ids, not taxonomic ranks. It is used to reduce the output to a set of taxa of specific interest, e.g. specify -ac 83333, 679895 if you are only interested in matches to Escherichia coli K12 or Escherichia coli BW25113.
It sounds like you are hoping for a feature that allows you to specify a taxonomic rank to report at? I have added new options
-ar <rank> and -br <rank>
that allows you to specify a taxonomic rank at which to report at. This will be available in the next release.
Yes, I would like to recover features from a specific taxonomic rank.
Thank you very much for the explanation!
I saw your response about the new
-ar <rank> and
-br <rank> options for the taxonomy2function tool. I checked out the recent release notes for MEGAN6 and didn’t spot any mention of it. Just curious, is that feature still on the horizon? Any idea when we might see it in action?
Thanks for all the hard work!
I just uploaded a new release (version 6.25.2,) that has the option in it