Command Line Interface

Installing the DNA Chisel python library automatically installs the dnachisel command line interface (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.

DNA Chisel Command Line Interface

  dnachisel <source> <target> [--circular] [--mute] [--with_sequence_edits]

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.
- A Genbank file. In this case, only the optimized sequence file is created.
  The with_sequence_edits option specifies that edits are also annotated in the
  Genbank file. Note that the filename must end with '.gb'.

Note: this CLI will be developed on a per-request basis, so don't hesitate to
ask for more handles and options on Github

Example to output the result to a genbank:

>>> dnachisel

Example to output the result to a folder:

>>> dnachisel optimization_report/