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TumorscapeReader

Connects 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
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,
metadata.timeout=0

case3 properties queryGenes (missing) (expecting failure)

databaseLocation=http://thiscannotbefound.fi


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