Running kevlar

The kevlar library can be invoked via a command-line interface or a Python API.

Command line interface

Once installed, the kevlar software can be invoked from the shell using the kevlar command. The kevlar command line interface (CLI) uses the subcommand pattern, in which a single master command supports several different operations by defining multiple subcommands (such as kevlar novel and kevlar partition). Invoke kevlar -h or kevlar --help to see a list of all available subcommands, and invoke kevlar <subcommand> -h to see detailed instructions for that subcommand. Comprehensive documentation of the kevlar CLI is also available here.

Starting with version 1.0, the CLI will be under semantic versioning.

Python interface

The main procedure of each kevlar subcommand is implemented as a generator function and can be executed programmatically. The following example shows how a standalone script or notebook would invoke the kevlar partition procedure.

fh ='novel-reads.augfastq.gz', 'r')
readstream = kevlar.parse_augmented_fastx(fh)
partitioner = kevlar.partition.partition(readstream, maxabund=200)
numreads_per_partition = [len(part) for partid, part in partitioner]
plt.hist(numreads_per_partition, bins=25)

It is also possible to mimic the behavior of the CLI with Python code. The following example shows how to execute kevlar partition from a standalone script or notebook.

arglist = [
    'partition', '--out', 'partitioned-reads.augfastq.gz',
    '--max-abund', '200', 'novel-reads.augfastq.gz'
args = kevlar.cli.parser().parse_args(arglist)

Other units of code in the kevlar package may also be useful for standalone Python programs. However, the Python API is not yet slated for semantic versioning and is not as stable or well documented as the CLI. Have fun and knock yourself out, but be prepared for changes in internal behavior in subsequent releases!