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.
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 Usage: 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 (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/