A program to generate reports for the distribution of functions across genomes.
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Generates TAB-delmited output files for functions from a single function annotation source across genomes.
For a simlar program that reports HMM hits across genomes, see anvi-script-gen-hmm-hits-matrix-across-genomes.
This program is very similar to anvi-display-functions, and can also perform a functional enrichment analysis on-the-fly if you provide it with an optional groups-txt file. Unlike, anvi-display-functions, this program will report TAB-delmited output files for you to further analyze.
You can run the program on a set of genomes for a given annotation source:
anvi-script-gen-function-matrix-across-genomes -e external-genomes \ --annotation-source COG20_FUNCTION \ --output-file-prefix MY-GENOMES
The command above will result in two files in your work directory, both of which will be of type functions-across-genomes-txt:
Alternatively you can run it with a groups-txt that associates sets of genomes with distinct groups,
anvi-script-gen-function-matrix-across-genomes -i internal-genomes \ --annotation-source COG20_FUNCTION \ --output-file-prefix MY-GENOMES \ --groups-txt groups.txt
which would generate an additional file in your work directory of type functional-enrichment-txt:
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