Settings - User Guide to SeqNinja

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.

Objective	Expression	Examples	Comments
Set the root directory for relative file paths used in the rest of the script	`!datapath` `!datapath:in` `!datapath:out`	`!datapath='C:\Users\MyName\data\'`	Relative path names are presumed relative to one of the following, in order: If set, `!datapath:in` (for input files) or `!datapath:out` (for output files). Otherwise, if set, `!datapath`. Otherwise, the working directory. Using different directories for input and output reduces risk of accidentally overwriting an input file.
Substitute setting values inside strings	`!setting`	`!setting:substitution=true`	‘True’ permits the substitution of setting values in a script; ‘false’ prohibits such substitution.
Specify a temporary files directory	`!tempdir`	`!tempdir='D:/temp'`	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	`!features`	`!features='CDS,source'`	See the notes below this table.
Set verbose output of the types specified in the value	`!verbose`	`!verbose='TRACE,DATA'`	This sets verbose output of the types specified in the value. This can be useful for providing progress information and for trouble-shooting.

Objective	Expression	Examples	Comments
Output an auxiliary file to preserve features during format conversion	`!conversion`	`!conversion=natural` `!conversion=full`	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	`!comments:history`	`!comments:history='on'` `!comments:history='off'`	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 `!conversion='full'` is set). A sequence history includes: When the sequence was created. The name of the sequence, if it has a name before written. A SeqNinja expression that can be used to create the sequence.

*Note 1: Other settings can affect the display of features resulting from use of !conversion and !features. For example, including !features=CDS above a statement with range endpoints will cause only CDS features to be displayed.

*Note 2: If you wish to set endpoints based on features that you want to later filter from the output, temporarily set !features=*. After setting the endpoints, change the !features setting to the type required for the desired output.

File patterns

Integral expressions

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