Command Line Interface

Installing the DNA Chisel python library automatically installs the dnachisel command line interace (CLI) accessible from the machine’s terminal.

This interface enables to get a problem as an annotated genbank and output the optimized sequence either as a single genbank or with a multi-file optimization report.

Type dnachisel -h to display the documentation below, and see the examples/cli directory for files to test the command line interface on.

DnaChisel Command Line Interface

Usage:
  dnachisel <source> <target> [--circular] [--mute]

Where ``source`` is a fasta or Genbank file, and target can be one of:
- A folder name or a zip name (extension .zip). In this case a complete report
  along with the sequence will be generated.

Note: this CLI will be developed on a per-request basis, so don't hesitate to
ask for more handles and options on Github
(https://github.com/Edinburgh-Genome-Foundry/DnaChisel/issues)

Example to output the result to a genbank:

>>> dnachisel annotated_record.gb optimized_record.gb

Example to output the result to a folder:

>>> dnachisel annotated_record.gb optimization_report/

Example to output the result to a zip archive:

>>> dnachisel annotated_record.gb optimization_report.zip