Exporting FASTA

FastaExporter Module in GLUE

The fastaExporter module in GLUE allows users to export nucleotide sequences from a set of Sequence objects into a FASTA file format.

Type-specific Commands:

Command	Description
export	Exports sequences to a FASTA file.
export-member	Exports sequences of alignment members to a FASTA file.
web-export	Exports sequences to a FASTA file via a web request.
web-export-member	Exports sequences of alignment members via a web request.

Example Configuration:

The module's configuration allows customization of the FASTA file output. An example configuration file might look like this:

<fastaExporter>
    <idTemplate>${gb_primary_accession}.${gb_gi_number}.${gb_length}</idTemplate>
</fastaExporter>

The idTemplate field utilizes FreeMarker templates to define the format of the FASTA headers. This feature provides users with flexibility to include specific metadata from their project’s database, such as GenBank accession numbers, sequence lengths, or other custom fields.

By modifying the template, users can adjust the information displayed in the FASTA header. For example, in phylogenetic analyses, users may include taxonomic labels or other relevant identifiers, ensuring that exported FASTA files meet their analytical needs. Use Case:

This module can be particularly useful when preparing data for phylogenetic tree construction. The ability to customize the FASTA headers with project-specific metadata, such as accession numbers and sequence lengths, provides clear, informative sequence identifiers when visualizing phylogenies.

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