Settings configure values used implicitly throughout the rest of the script, and always begin with an exclamation mark (!). The value of settings may be a single word, or a quoted string using single or double quotes. In a setting, double quoted strings are not interpreted as sequences.
Built-in settings are shown in the table below. You can also use setting substitution.
|Set the root directory for relative file paths used in the rest of the script||
|| Relative path names are presumed relative to one of the following, in order:
|Substitute setting values inside strings||
||‘True’ permits the substitution of setting values in a script; ‘false’ prohibits such substitution.|
|Specify a temporary files directory||
||This can be used to put temporary files on a drive with more space, or in a more accessible location.|
|Filter output features to those listed||
||See the notes below this table.|
|Set verbose output of the types specified in the value||
||This sets verbose output of the types specified in the value. This can be useful for providing progress information and for trouble-shooting.|
|Output an auxiliary file to preserve features during format conversion||
||See Convert Between Annotated and Featureless Formats. Also see the notes below this table.|
|Specify whether to record a sequence history in the comments section of generated sequences||
|| Sequence history is only written when comments can be written to the output format. A sequence history can be written for GenBank files, Lasergene files, and FASTA files (when
A sequence history includes:
Need more help with this?