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Up: Component summary
Component
TumorscapeReaderConnects to the Tumorscape database and outputs chromosomal aberration information for the query genes. The input is a list of HUGO gene names. Outputs are descriptional statistic from Tumorscape stating the recurrence of the query genes in different types of cancer.
Leaving the queryGenes input empty will query all the genes in the database.
Since the database is only available as an ftp stored zip-file, recurrent queries are slow. Saving a local copy of the database zip-file and using this in the databaseLocation parameter is highly recommended.
| Version | 2.0 |
|---|---|
| Bundle | microarray |
| Categories | Annotation |
| Authors | Riku Louhimo (Riku.Louhimo@Helsinki.FI) |
| Issue tracker | View/Report issues |
| Requires | Asser.jar (jar) ; commons-io-2.0.1.jar (jar) ; commons-net-3.2.jar (jar) |
| Source files | component.xml TumorscapeReader.java |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| queryGenes | IDList | Optional | HUGO names for query genes. |
| database | ZIP | Optional | Zip-file containing the Tumorscape database. This overrides the 'databaseLocation' parameter. |
Outputs| Name | Type | Description |
|---|---|---|
| features | CSV | Tab-delimited descriptions on the recurrent copy number aberrations in different cancers at which the query genes are present. |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| databaseLocation | string | "ftp://ftp.broadinstitute.org/pub/cancer/gcnmp/Summary_data/Gene_summary_pages/Tumorscape_webfiles_20100104.zip" | URL to Tumorscape database. The 'database' input overrides this parameter. A local location can also be given by starting with 'file:'. |
Test cases| Test case | Parameters▼ | IN queryGenes |
IN database |
OUT features |
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|---|---|---|---|---|---|---|
| case1 | properties | queryGenes | database | features | ||
| case2_inputNotFound | properties | queryGenes | (missing) | features | ||
|
databaseLocation=ftp://ftp.broadinstitute.org/pub/cancer/gcnmp/Summary_data/Gene_summary_pages/Tumorscape_webfiles_20100104.zip, |
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| case3 | properties | queryGenes | (missing) | (expecting failure) | ||
|
databaseLocation=http://thiscannotbefound.fi |
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