7. Sumup table

To make the output of the pipeline easier to use and more accessible, A table of unitigs - genes - functions - clade is built. For each gene detected by Prodigal, the user is given the unitig from which it comes, its translated sequence, KO term and function if available from the output of MicrobeAnnotator, and its taxonomic assignation:

User may then decide to take interest into a particular species:

grep -F 'Prevotella copri' case_unitigs_to_clade_and_gene_functions.tsv

Maybe look for a function:

grep -F '2-amino-4-deoxychorismate dehydrogenase [EC:1.3.8.16]' case_unitigs_to_clade_and_gene_functions.tsv

Or get an overview of the functions found:

cut -f6 case_unitigs_to_clade_and_gene_functions.tsv | sort | uniq -c | sort -g
#gives you each function and the number of times it appears, sorted 
#you can do the same with species !

Maybe look fo KO terms:

grep -F -f list_ko_one_per_line.txt case_unitigs_to_clade_and_gene_functions.tsv