search

wwood / singlem

Novelty-inclusive microbial community profiling of shotgun metagenomes
http://wwood.github.io/singlem/
GNU General Public License v3.0
136 stars 17 forks source link

using combined singlem pipe output #77

Open slambrechts opened 3 years ago

slambrechts commented 3 years ago

Hi,

I read that several OTU tables can be combined into one, but that this is not necessary if the combined output is to be input again into summarise. My question is whether I can? Can I use a combined otu table as input when for example using singlem summarise --rarefied_output_otu_table, or should I rather specify all the original otu tables? And in the latter case, can I use an asterisk? Like for example: 

singlem summarise --input_otu_tables *.csv --output_otu_table combined.otu_table.csv

singlem summarise --input_otu_tables combined.otu_table.csv --rarefied_output_otu_table rarefied.combined.otu_table.csv

singlem summarise --input_otu_tables rarefied.combined.otu_table.csv --biom_prefix myprefix

Best, Sam

wwood commented 3 years ago

Hi,

Either should work fine. BTW, the * is intepreted by bash, not singlem. SingleM just sees a list of strings in its sys.argv.

I'll leave this issue open until the doco improves. Thanks, ben