Operation

Output

Applies to:  Any data object (except Priors Generators and other Output data objects)
Returns: Output Data

Description

Outputs data items to text documents in selected data formats. The document will be wrapped in a so-called "Output Data" object and the contents of this can be saved to files. If MotifLab is run in CLI-mode (without the GUI), all Output Data objects that are created during the execution of a protocol script will automatically be saved to files after completion of the protocol (the filename will be the name of the data object with a suffix determined by the data format used). If no target Output data object is specified for the output operation, a new Output object will be created automatically and assigned a default name consisting of the prefix "Output" followed by an incremental number. If a target Output data object is specified and it already exists, the output will be appended to that object if possible. If it is not possible to append more text to this data object (because it is formatted in a data format that does not allow additional text to be appended, such as HTML-formats), the operation will end with an error. When Feature Datasets are output, the sequences will be output in the order they are currently sorted.

Graphics output
Output saved in Excel and HTML formats may include graphics, such as charts and motif logos. In Excel, these graphics will always be embedded in the file itself, but in HTML format you have a few options on how to output motif and module logos. Please refer to the HTML format documentation for more information.

Direct output
Version 2.0+ of MotifLab allows the output operation to be used to output literal text strings directly to output objects (but only within protocols). The format is: <Output object> = output "some text string...". The text string enclosed in double quotes can contain references to data objects on the form "{dataobject} and the value of the referenced object will then be included in the output as explained in the documentation for the Template and TemplateHTML data formats (the same formatting-options for referenced objects are also available). The text string can also contain TABs, newlines, double quotes and backslashes if these are properly escaped as \t, \n, \" and \\ respectively.

Arguments

NameDescription
format The data format to use for the output. The type of the data object will determine which formats are available.
output parameters Each data format can have additional format specific parameter settings. See the documentation for the data format for more information.

Examples


# Outputs the DNA Sequence Dataset called 'DNA' in FASTA format (with default settings) to a new output object provided with a default name
output DNA in FASTA format

# Outputs regions from the TFBS track in GFF-format (with genomic rather than relative coordinates) to an Output data document called 'Sites' (or appends the output to this document if it already exists)
Sites = output TFBS in GFF format {Position="Genomic"}

# Outputs motifs in the motifcollection in a format with 4 rows and N columns (with columns separated by commas)
output MotifCollection3 in RawPSSM format {Orientation="Horizontal",Delimiter="Comma"}

# Outputs the string 'Hello world! The value of X is' followed by the actual value of the data object named X (v2.0+)
output "Hello world! The value of X is {X}!"


See Also: Output Data, FASTA, GFF, EvidenceGFF, BED, WIG