optional arguments:

-h, --help

show this help message and exit

Input options:

-t TRAITS, --traits TRAITS

Input trait table (comma-separated-values). Trait presence is indicated by 1, trait absence by 0. Assumes strain names in the first column and trait names in the first row

-g GENES, --genes GENES

Input gene presence/absence table (comma-separatedvalues) from ROARY. Strain names must be equal to those in the trait table

-n NEWICKTREE, --newicktree NEWICKTREE

Supply a custom tree (Newick format) for phylogenetic analyses instead instead of calculating it internally.

-s START_COL, --start_col START_COL

On which column in the gene presence/absence file do individual strain info start. Default=15. (1-based indexing)

--delimiter DELIMITER

The delimiter between cells in the gene presence/absence and trait files, as well as the output file.

-r RESTRICT_TO, --restrict_to RESTRICT_TO

Use if you only want to analyze a subset of your strains. Scoary will read the provided comma-separated table of strains and restrict analyzes to these.

Output options:

-o OUTDIR, --outdir OUTDIR

Directory to place output files. Default = .

-u, --upgma_tree

This flag will cause Scoary to write the calculated UPGMA tree to a newick file

-p P_VALUE_CUTOFF [P_VALUE_CUTOFF ...], --p_value_cutoff P_VALUE_CUTOFF [P_VALUE_CUTOFF ...]

P-value cut-off / alpha level. For Fishers, Bonferronis, and Benjamini-Hochbergs tests, SCOARY will not report genes with higher p-values than this. For empirical p-values, this is treated as an alpha level instead. I.e. 0.02 will filter all genes except the lower and upper percentile from this test. Run with "-p 1.0" to report all genes. Accepts standard form (e.g. 1E-8). Provide a single value (applied to all) or exactly as many values as correction criteria and in corresponding order. (See example under correction). Default = 0.05

-c [{I,B,BH,PW,EPW,P} [{I,B,BH,PW,EPW,P} ...]], --correction [{I,B,BH,PW,EPW,P} [{I,B,BH,PW,EPW,P} ...]]

Apply the indicated filtration measure. Allowed values are I, B, BH, PW, EPW, P. I=Individual (naive) p-value. B=Bonferroni adjusted p-value. BH=BenjaminiHochberg adjusted p. PW=Best (lowest) pairwise comparison. EPW=Entire range of pairwise comparison p-values. P=Empirical p-value from permutations. You can enter as many correction criteria as you would like. These will be associated with the p_value_cutoffs you enter. For example "-c I EPW -p 0.1 0.05" will apply the following cutoffs: Naive p-value must be lower than 0.1 AND the entire range of pairwise comparison values are below 0.05 for this gene. Note that the empirical p-values should be interpreted at both tails. Therefore, running "-c P -p 0.05" will apply an alpha of 0.05 to the empirical (permuted) p-values, i.e. it will filter everything except the upper and lower 2.5 percent of the distribution. Default = Individual p-value. (I)

-m MAX_HITS, --max_hits MAX_HITS

Maximum number of hits to report. SCOARY will only report the top max_hits results per trait

--include_input_columns GRABCOLS

Grab columns from the input Roary file. and puts them in the output. Handles comma and ranges, e.g. --include_input_columns 4,6,8,16-23. The special keyword ALL will include all relevant input columns in the output

-w, --write_reduced

Use with -r if you want Scoary to create a new gene presence absence file from your reduced set of isolates. Note: Columns 1-14 (No. sequences, Avg group size nuc etc) in this file do not reflect the reduced dataset. These are taken from the full dataset.

--no-time

Output file in the form TRAIT.results.csv, instead of TRAIT_TIMESTAMP.csv. When used with the -w argument will output a reduced gene matrix in the form gene_presence_absence_reduced.csv rather than gene_presence_absence_reduced_TIMESTAMP.csv

Analysis options:

-e PERMUTE, --permute PERMUTE

Perform N number of permutations of the significant results post-analysis. Each permutation will do a label switching of the phenotype and a new p-value is calculated according to this new dataset. After all N permutations are completed, the results are ordered in ascending order, and the percentile of the original result in the permuted p-value distribution is reported.

--no_pairwise

Do not perform pairwise comparisons. Inthis mode, Scoary will perform population structure-naive calculations only. (Fishers test, ORs etc). Useful for summary operations and exploring sets. (Genes unique in groups, intersections etc) but not causal analyses.

--collapse

Add this to collapse correlated genes (genes that have identical distribution patterns in the sample) into merged units.

Misc options:

--threads THREADS

Number of threads to use. Default = 1

--test

Run Scoary on the test set in exampledata, overriding all other parameters.

--citation

Show citation information, and exit.

--version

Display Scoary version, and exit.

by Ola Brynildsrud (olbb@fhi.no)