Sequence Manipulation in GLUE - giffordlabcvr/Parvovirus-GLUE GitHub Wiki

User Guide: Importing, Browsing, and Exporting Sequence Data in GLUE

This guide outlines how to manage sequence data in GLUE, covering the import and export of sequences, as well as browsing options.

1. Importing Sequence Data using the import source Command

The default way to import sequence data into a GLUE project is by using the import source command. This command expects a folder containing individual sequence files, either in FASTA or GenBank XML format. When importing FASTA files, the sequence header will be used as the sequence ID, and it is recommended to name the files by their sequence IDs to ensure clarity and consistency.

Here is an example of the import source command:

   Mode path: /
   GLUE> run file buildCoreProject.glue

In this example, the system imports sequences from the specified folder, recognizing each file format (in this case, GenBank XML) and assigning the appropriate sequenceID based on the file contents. If the files were in FASTA format, the sequence header would be treated as the sequenceID.

This approach allows for streamlined sequence data management, especially when working with large datasets organized by sequence identifiers.

2. Other Ways to Import Sequence Data

Module Type: fastaImporter

The fastaImporter module allows you to import nucleotide data from a FASTA file, creating a set of Sequence objects.

  • Type-Specific Commands:

    • import: Imports sequences from a FASTA file.

  • Usage Example:

GLUE> import path/to/sequences.fasta

General Module Mode Commands: In addition to the above command, all general module mode commands are available for use after importing.

  1. Exporting Sequence Data

Module Type: fastaExporter

The fastaExporter module enables you to export nucleotide data from a set of Sequence objects to a FASTA file.

Type-Specific Commands:
    export: Exports sequences to a FASTA file.
    export-member: Exports the sequences of alignment members to a FASTA file.
    web-export: Exports sequences to a FASTA file via web interface.
    web-export-member: Exports the sequences of alignment members to a FASTA file via web interface.
  • Usage Example:
GLUE> import path/to/sequences.fasta