An Output Data object is a document in some specific data format. It is mostly just used to represent the information held by other data objects in text based formats that can later be saved to files, since data objects in MotifLab cannot otherwise be saved to files directly (in their internal representation). Output Data objects can also hold more complex documents containing extensive reports, in for example HTML format, that can contain embedded content, such as e.g. images.

Output Data objects are displayed in separate tabs in the main panel of the GUI, with the tabs themselves showing the names of the data objects. The contents of Output Data objects can be saved to files by selecting either "Save", "Save As..." or "Save All" from the file menu. Unless otherwise specified, the names of the output files will be based on the names of the data objects, and the file suffix will be determined from the data format used when creating the Output Data object. If MotifLab is run in CLI-mode, all Output Data objects created during the execution of the protocol (that have not been explicitly deleted) will automatically be saved to files afterwards, unless the "-no_output" option is specified.

In the GUI, individual Output objects can be deleted by clicking on the close icons of their tabs, and you can delete all Output objects by selecting "Close All Output Panels" from the "View" menu or by selecting either "Clear Data ⇒ Other Data" or "Clear All Data" from the "Data" menu.

Output Data objects can be of three main types: text ("raw text"), HTML or binary formats. The first two of these can be displayed directly in MotifLab's GUI, but documents in binary formats (e.g. Excel formats or PDF) cannot be displayed by MotifLab. However, binary formatted documents can still be saved to files and reopened later in external viewers, such as Excel or Adobe Acrobat.

Creating Output Data

Output Data objects can only be created from other data objects using the output operation after selecting which format to use. Objects in most "raw text" formats will allow their documents to be appended to later, but binary and HTML-formatted documents will not.

Examples

# Output the contents of a DNA track object (feature dataset) in FASTA format Output1 = output DNA in FASTA format # If no target Output Data object is specified, the output will be stored in an object called "Results" output DNA in Plain format # First output the contents of a TFBS track object in BED format to the Output Data object "Output2", # then append the contents of a second TFBS track in GFF format to the same document Output2 = output TFBS in FASTA format Output2 = output TFBS2 in GFF format # Output the contents of a DNA track object (feature dataset) in FASTA format Output1 = output DNA in FASTA format

Modifying Output Data

If the current contents of an Output Data object allows it, new text can be appended to the end of the document by applying additional output operations that write to the same Output Data object. However, existing parts of a document cannot be modified after they have been added.

Using Output Data

Output Data objects can be viewed by the user in MotifLab's GUI. This can be nice for analysis output and similar report-like documents, but the main purpose of most Output Data objects is just to function as temporary storage of another data object in a format that can be saved to file. Like Text Variables, Output Data objects containing text in a supported input data format can also be parsed to create other objects with the new operation.

HTML dependencies

Output Data objects in HTML formats may include embedded content, such as images, CSS style sheets and JavaScript (JS) files, that must also be saved – perhaps to separate files – when the HTML document itself is saved. How this is done is controlled in different ways.

CSS and JavaScript
The way CSS and JS content is handled can be controlled by selecting "Options..." from the "Configure" menu and then going to the "HTML" tab.

None: CSS and/or JS will not be included at all. This may result in some functionality not working properly.
Shared File: CSS will be saved to a file named "motiflab_style.css" and JavaScript will be saved to "motiflab_script.js" in the same directory as the main output file. If these files exist already, they will not be created anew. This means that if you save additional HTML files to the same directory, they can all share these CSS/JS-files.
New File: CSS and/or JS will always be saved to new files named after the main output file with an added incremental number suffix. E.g. if the main file is called "report.html", the dependencies could be named "report_1.js" and "report_2.css".
Link: The HTML document will reference CSS and/or JS files located on the MotifLab web server. This will save some disc space locally but may be risky if the MotifLab web server goes down.
Embed: CSS and/or JS will be included directly in the HTML document itself rather than being stored in separated files.

The style sheet to use can be chosen in the same dialog by selecting a CSS-file from disc, or by selecting one of the predefined style sheets included with MotifLab (currently only [default] and [green]).

Motif logos (and module logos)
Motif logos are graphical representations of the binding preferences for different nucleotide bases each at each position in the TF motif. Many analyses contain tables with results for individual motifs, and when outputting such analyses in HTML format, the logos for these motifs can optionally be included as images. The way this is done is usually decided when executing the output operation using the "Logos" data format parameter.

No: Motif logos (or module logos) will not be included in the output at all.
Text: Rather than a colorful graphical representation, the logos will rendered using pure text instead (for example as an IUPAC consensus sequence). No extra image files will be saved with this option.
Shared Files: The motif/module logos will be saved to files named after the motifs/modules themselves in the same directory as the main output file. If files with the same names already exist in that directory they will not be created anew. This means that if you save additional HTML files to the same directory that also include logos for the same motifs/modules, they can all share these image files.
New Files: The motif/module logos will always be saved to new image files named after the main output file with an added incremental number suffix. E.g. if the main file is called "report.html", the logo files could be called "report_3.gif", "report_4.gif", report_5.gif", etc.