pangenome Functional Enrichment Analysis from Roary
Help message:
python panFEAR.py -h
usage: panFEAR.py [-h] [-gpa GENE_PRESENCE_ABSENCE] [-fhp] [-b N_BINS]
[-up UPPER_PERCENT] [-lp LOWER_PERCENT] [-c CORRECTION]
[-o OUTPUT_FOLDER]
optional arguments:
-h, --help show this help message and exit
-gpa GENE_PRESENCE_ABSENCE, --gene_presence_absence GENE_PRESENCE_ABSENCE
Roary output file "gene_presence_absence.csv" from
which information is retrieved
-fhp, --filter_hypothetical_proteins
Flag for excluding "hypothetical protein" from the
analysed functions
-b N_BINS, --n_bins N_BINS
Number of bins in the pangenome
-up UPPER_PERCENT, --upper_percent UPPER_PERCENT
Upper percent among the pangenome of the group of
which panFEAR analyses functional enrichment
-lp LOWER_PERCENT, --lower_percent LOWER_PERCENT
Lower percent among the pangenome of the group of
which panFEAR analyses functional enrichment
-c CORRECTION, --correction CORRECTION
P-value correction method from multiple tests bias
-o OUTPUT_FOLDER, --output_folder OUTPUT_FOLDER
ABSOLUTE! path where to store the produced outputs