This example assumes familiarity with a few other commands in the CLI to create the input file containing the genomes to be put in the new genome group. You do not need to be familiar with these commands, just the format of the input file. The format of the input file is simply a list of genome ids, one per line with no other information in the file.
$ p3-all-genomes --in genome_name,aureus > Staphylococcus.aureus.genomes $ p3-all-genomes --in genome_name,Staphylococcus > Staphylococcus.all.genomes $ a_not_b Staphylococcus.all.genomes Staphylococcus.aureus.genomes > Staphylococcus.not.aureus.genomes $ wc *.genomes 9257 41089 399759 Staphylococcus.all.genomes 8383 36955 356756 Staphylococcus.aureus.genomes 876 4146 43099 Staphylococcus.not.aureus.genomes 18516 82190 799614 total
Let's take a quick look at a few entries in each file using the unix head command. In this case, the first five lines of each file are displayed. Notice that the header exists in two of the three files. It is not in the file created with the a_not_b command because the header appeared in both input files to the a_not_b command.
$ head -n 5 *.genomes ==> Staphylococcus.all.genomes <== genome.genome_id 904758.3 904731.3 904739.3 904750.3 ==> Staphylococcus.aureus.genomes <== genome.genome_id 904758.3 904731.3 904739.3 904750.3 ==> Staphylococcus.not.aureus.genomes <== 1000590.6 1008454.3 1034809.4 1078083.3 1115805.3
The input files to create genome groups are almost ready. The input to p3-put-genome-group is a single column file with the only values being genome ids. The header needs to be removed. We can easily do this with an editor, or use the unix grep command with the -v option. For this example, we will just edit the file with an editor and remove the header.
The p3-put-genome-group takes the list of genome ids on standard input. Using the unix cat command we can send the contents of our newly created files of genome ids to the p3-put-genome-group command with the following command.
$ cat Staphylococcus.not.aureus.genomes | p3-put-genome-group "Staphlococcus not aureus" $ cat Staphylococcus.aureus.genomes | p3-put-genome-group "Staphylococcus aureus"
The two newly created genome groups are now visible and usable in your workspace using on the PATRIC web site, as well as accessible using the command line interface.
$ p3-get-genome-group "Staphylococcus aureus" 904758.3 904731.3 904739.3 904750.3 904763.3 904725.3 904734.3 904737.3 904754.3 904768.3 <...>