The Write Features template, located in the Templates panel, is used to create a SeqNinja feature table or VCF file using the annotations from a specified sequence file. The output features files can be used with other SeqNinja scripts, such as Map Features.
When you choose this template, you are immediately prompted to open a sequence from a file chooser dialog. After making a selection, the Feature File Type dialog appears. Make a choice from the list.
Press Run to fill in the template based on your selections and create the feature file immediately or Make to fill in the template without running.
Choose Make to review the information and make any necessary changes before pressing Run:
- To change the source sequence, use the Choose Sequence(s) button (see Add and modify a sequence). To select a particular sequence from the file, rather than the entire file (default), make a selection from the adjacent drop-down menu.
- To change the output format, make a selection from the Format drop-down menu. Most available options will save the output as a sequence file. The final two options—*SeqNinja Feature Table* and *VCF*—will instead save the output as a feature file.
- To specify the name and location in which to save the output (see Specify output format and location) press the Save Results As button and select a location.
- If you specified VCF in the output popup (discussed in the second bullet point, above), or select VCF from the Format drop-down menu, you must provide a sequence annotated by SeqNinja with variants from a VCF file. This is done in the row that appears under the Save Results As row. Check the Use as template box, then click Browse to navigate to the VCF file. The template may be used as a guide to the construction of the result file. For example, the meta-information lines may be copied from the template to the result file.
After setting up the template as desired, click Run to run the script and create a feature file. Or choose Cancel to exit from the template without running the script.
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