I have used the MG-Rast tools python code to download summary tables of sequence hits that fall into different Subsystems ontology categories. For instance, the following code summarizes 5 samples, compiles and downloads a table that is easily then read into other software:
mg-compare-functions.py \ --ids "mgm4812503.3,mgm4812531.3,mgm4812526.3,mgm4812553.3,mgm4812451.3" \ --level level3 \ --source Subsystems \ --format text \ --evalue 10 > ~/Desktop/PhD/Metagenome/Download/mgRast_ontologyLVL3_list01.txt
I've removed my authentication token so this isn't exactly reproducible, but it makes a tab delimited text file that looks something like this:
mgm4812451.3 mgm4812503.3 mgm4812526.3 mgm4812531.3 mgm4812553.3 COG2363 25684 20011 29927 25736 15503 Carboxysome 6459 5200 7519 6074 4606 Respiratory_dehydrogenases_1 21806 19178 28776 21040 15472 Iron_acquisition_in_Vibrio 14557 14243 15804 12768 8607 Transport_of_Iron 7202 7436 8432 6641 5235
I'm trying to get a similar set of summary annotation tables for organisms from mg-Rast, but I can't find an analogous tool to the mg-compare-functions.py tool but for organisms. I have ~320 samples that I'd like to quickly compile into a table of summary hits by organism ID at roughly the genus level. How should I do this?