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