Up: Component summary Component

JASPARMotif

Writes JASPAR motif matrices into a MotifSet directory. Fetching of motifs is based on different optional filters, which correspond to the fields of JASPAR database. Any field can be used as a filter with the IDs input (and idType parameter). Species and class fields are included as parameters for convenience. If none of these are given the component fetches all the matrices in the given JASPAR database.

Version 2.0.3
Bundle microarray
Categories Sequence Motif
Authors Viljami Aittomaki (viljami.aittomaki@helsinki.fi)
Issue tracker View/Report issues
Requires Java
Source files component.xml JASPARMotif.java
Usage Example with default values

Inputs

Name Type Mandatory Description
IDs IDList Optional List of ID's for motifs to get from JASPAR. ID's can represent any single field in JASPAR (e.g. id or name). The field name must be specified with the 'idType' parameter! Omitting this input means no filtering based on IDs.

Outputs

Name Type Description
motifs MotifSet A directory containing the motifs fetched from JASPAR in Anduril compatible format. Files are named by motif name.
annotations AnnotationTable A file containing annotations for each fetched motif. Has columns "name", "id", "version", "class", "family", "species", "collection", "acc", "medline", "pazar_tf_id", "type", and "comment". Explanations of the columns can be found in JASPAR documentation.

Parameters

Name Type Default Description
collection string "CORE" Comma-separated list of JASPAR collections to include. Empty string means no collection based filtering. Usually the CORE collection is the right one.
flatFileURL string "http://jaspar2014.genereg.net/html/DOWNLOAD/ARCHIVE/JASPAR2010/all_data/FlatFileDir/" URL of a flat file version of JASPAR. The URL should point to a FlatFileDir version of JASPAR (and not e.g. a sql_tables version). The JASPAR website has several different flat file versions of the database.
idType string "" Type of ID's that are in input list 'IDs'. This parameter must be defined (not empty) if 'IDs' is present! Valid values are field names present in the database.
motifClass string "" Comma-separated list of structural classes of motifs to include. Empty string means no class based filtering.
species string "9606" Comma separated list of species to include (motifs for other species are filtered out). Use NCBI tax IDs (e.g. 9606 for human) or a dash ("-") to match motifs with no annotated species. Empty string means no species based filtering. Only integers and the dash are valid values (or empty)!

Test cases

Test case Parameters IN
IDs
OUT
motifs
OUT
annotations
case1-idFile properties IDs motifs annotations

idType=id,

case2-parameterFiltering properties (missing) motifs annotations

motifClass=Zinc-coordinating,
collection=CORE,
flatFileURL=http://jaspar2014.genereg.net/html/DOWNLOAD/ARCHIVE/JASPAR2010/jaspar_CORE/non_redundant/all_species/FlatFileDir/,
species=-,6239,


Generated 2018-12-16 07:42:09 by Anduril 2.0.0