Up: Component summary
Up: Component summary
Component
JASPARMotifWrites 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 |
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|---|---|---|---|---|---|---|
| case1-idFile | properties | IDs | motifs | annotations | ||
|
idType=id, |
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| case2-parameterFiltering | properties | (missing) | motifs | annotations | ||
|
motifClass=Zinc-coordinating, |
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