Outputs

Tabular¶

The main output of the assembly typing mode is a tab-delimited table of the results. See the api for an explanation of the column content.

The default is to print this table to stdout. You can use UNIX redirection operators (> or >>) or the -o/--out flag to write to a file.

If the summary table already exists and is not empty, Kaptive will append to it (not overwrite it) and suppress the header line. This allows you to run Kaptive in succession on sets of assemblies, all outputting to the same table file.

To disable the tabular output, simply redirect the output to /dev/null.

Fasta¶

The -f/--fasta flag produces a fasta file of the region(s) of the assembly which correspond to the best locus match. This may be a single piece (in cases of a good assembly and a strong match) or it may be in multiple pieces (in cases of poor assembly and/or a novel locus).

You can specify either a directory, which will write one file per assembly named as {assembly}_kaptive_results.fna, or a single file ("-" for stdout), which will write all the sequences to that file.

For example:

kaptive assembly kpsc_k assembly.fasta -f

This results in default behaviour which will produce one file per assembly in the current directory. However, to specify a directory:

kaptive assembly kpsc_k assembly.fasta -f kaptive_results/

or for a single file, both are valid:

kaptive assembly kpsc_k assembly.fasta -f kaptive_results.fna
kaptive assembly kpsc_k assembly.fasta -f - > kaptive_results.fna

JSON¶

The -j/--json flag produces a JSON file of the results which allows Kaptive to reconstruct the TypingResult objects after a run which can be used with kaptive-convert. Unlike previous version (2 and below), this is a JSON lines file (or "-" for stdout), where each line is a JSON object representing the results for a single assembly. If the file already exists, Kaptive will append to it (not overwrite it).

The default is to write this file to: kaptive_results.json, however the path can be specified after the flag, for example:

kaptive assembly kpsc_k assembly.fasta -j kaptive_results.json

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