ska info - simonrharris/SKA GitHub Wiki
The info subcommand prints some summary statistics for one or more split kmer files.
The output can be in a verbose or tabulated (using -t flag) format.
| Column | Description |
|---|---|
| File | The name of the split kmer file |
| Kmers Size | The kmer size in the file |
| # samples | Number of samples in the file |
| # kmers | Number of kmers in the file |
| # sample patterns | Number of sample patterns in the file |
Verbose output prints the same information in a longer form, but also prints the names of all samples in the file.
merged.skf
==========
Kmer size: 15
Number of samples: 30
Sample names:
101259, 101260, 101261, 101262, 101263, 101264, 101266, 110944,
110945, 110946, 110947, 110948, 110949, 110950, 110951, WHO_F,
WHO_G_with_plasmids, WHO_K_with_plasmids, WHO_L_with_plasmids, WHO_M_with_plasmids, WHO_N_with_plasmids, WHO_O_with_plasmids, WHO_P_with_plasmids, WHO_U_with_plasmids,
WHO_V_with_plasmids, WHO_W_with_plasmids, WHO_X_with_plasmids, WHO_Y_with_plasmids, WHO_Z_with_plasmids, ERR2172296
Number of kmers: 2819105
Number of sample patterns: 12515
File Kmer size # samples # kmers # sample patterns
merged.skf 15 30 2819105 12515
ska info [options] <split kmer files>
Options:
-h Print this help.
-f <file> File of split kmer file names. These will be added to or
used as an alternative input to the list provided on the
command line.
-t Print tabulated output.