Usage

Run analysis using canSNPer2

CanSNPer2 
    --database <path_to><database_name>               ## CanSNPer2 database file
    --refdir test/references/                         ## directory where references are located if not present see CanSNPer2-download
    --export (export snpfile)                         ## output snpfile
    -o results                                        ## output directory
    --save_tree <prefix>                              ## prefix for CanSNPer2 tree output (pdf)
    --tmpdir /tmp/                                    ## Select tempdir default global tmp
    *.fa                                              ## Any number of fasta files to run

Modify database

CanSNPer2-database 
    --database <path_to><database_name>               ## CanSNPer2 database file
    --mod_file <path_to><modification tree (1)>       ## node updates (1)
    --annotation <path_to><snp annotations (2)>       ## snp annotations (2)
    --log database/logs                               ## log directory
    --parent "A/M.1"                                  ## If replacing a branch add parent and replace
    --replace                                         ## Flag to replace a whole branch from --parent

Create a custom database

CanSNPer2-database 
    --database <path_to><database_name>               ## CanSNPer2 database file 
    --tree <CanSNPer[1/2]_tree file>                  ## Format (1) or cansnper1 formatted file
    --annotation <CanSNPer[1/2]_snpfile>              ## snp annotations (2)
    --reference <CanSNPer2_genomesfile>               ## Annotation of genome references to which snps are annotated (4)
    --source_type CanSNPer(if CanSNPer1)              ## If input is formatted according to cansnper1
    --create 
    --log <path to log folder>

Download genome references

CanSNPer2-download 
    --database <path_to><database_name>               ## CanSNPer2 database file (must have genome annotation loaded)
    --source genbank                                  ## Source refseq or genbank
    --outdir references                               ## reference directory (default ./reference)