Standard import
The Standard Import tool can import data from many standard bioinformatics formats, as well as tabular and text formats.
Launching Standard Import
Standard Import can be launched in a number of ways:
- Click the Import (
) icon in the Toolbar and choose Standard Import from the list presented.
- Use the menu option File | Import () | Standard Import ().
- Drag files from a file browser and drop them into the Navigation Area. Using this method:
- Standard Import runs without opening a configuration dialog.
- File formats are automatically detected (details below). To manually specify a format, launch the tool using one of the first two options in this list.
- Copy text, select a folder in the Navigation Area to import to, and paste the clipboard content. Using this method:
- Standard Import runs without opening a configuration dialog.
- The format of the text is automatically detected (details below). To manually specify a format, launch the tool using one of the first two options in this list.
Note: Copy/pasting can be an error prone operation. Importing from files is generally recommended.
Automatic format detection
By default Standard Import automatically detects each file's format based on a combination of the file name extension (e.g. .fa for fasta) and the format of the file's contents. The corresponding importer is then run. The imported element's history includes the name of the importer used.
When no supported format is detected, the file is imported as an external file. See Working with non-CLC format files for details about working with such files.
Using automatic format detection, files with different formats can be imported in a single run of the Standard Import tool.
Configuring Standard Import
When configuring Standard Import, click Add files to select files to import, or click Add folders to specify folders containing the files to import (figure 7.1).
When the Automatic import option is selected, file formats will be automatically detected, as described above.
To manually specify an importer, select the Force import as type option and choose the relevant format from the drop-down list.
The Force import as external file option is useful when a file's contents could be recognized as a supported format, but the aim is import the file as it is, rather than importing the contents to a CLC element. See Working with non-CLC format files for details about working with such files.
Figure 7.1: The Standard Import tool.
Importing sequence attributes using Standard Import
The information about a sequence that can be stored within a sequence file, and how structured that information is, depends on the file format.
Formats with generally agreed upon content rules allow for information to be extracted and placed into corresponding sequence attributes during import. For example, attributes such as a accession, organism, and description can be reliably extracted from GENBANK and EMBL format files.
A contrasting example is FASTA format, where there is no single convention for the header line contents. Thus, fairly basic rules are used to handle FASTA header lines, with the details depending on the presence of pipe symbols:
- No pipe symbols: Everything before the first space or tab is imported as the sequence name. Everything after is imported as the description.
- A single pipe symbol: Everything before the pipe symbol is imported as the sequence name. Everything after is imported as the description.Â
- Multiple pipe symbols: Everything up to and including the last pipe symbol is imported as the sequence name. Everything after is imported as the description.Â