Name: tm2cbio
Owner: The Hyve
Description: Utility to translate tranSMART export files to a directory ready for import to cBioPortal
Forked from: j-hudecek/tm2cbio
Created: 2015-07-22 15:09:24.0
Updated: 2015-07-22 15:09:24.0
Pushed: 2015-06-29 12:52:32.0
Homepage: null
Size: 484
Language: Groovy
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Utility to translate tranSMART export files to a directory ready for import to cBioPortal
Importer uses leaf concept nodes as names for clinical attributes where possible. If two concepts have the same leaf name, distinguishing parts of the concept path are added. This can be further customized by mapping concept to column name replace
.
If tranSMART ontology contains “special attributes” that cBioPortal recognizes (e.g. age, sex, for a list see mapping file), you can specify where in the ontology tree are they stored and what conversion and/or text replacements need to be applied.
All attributes are imported as STRING by default. INT and BOOLEAN can be specified using the mapping type
configuration followed by a concept path. for example
mapping type \Crizotinib PF2341066\IC50=INT
To run the utility you need a log4j and groovy installed. You can run it with
wget https://archive.apache.org/dist/logging/log4j/1.2.17/log4j-1.2.17.jar
groovyc -cp .:log4j-1.2.17.jar src/org/transmart/tm2cbio/*groovy
java -cp $GROOVY_HOME/embeddable/groovy-all-2.3.8.jar:. org.transmart.tm2cbio.Main tm2cbio.mapping.GSE4922.txt
You will need to replace 2.3.8 with the version of Groovy you have installed