README

cgData - Cancer Genome Browser Input/Output tools


This python module is designed to do tasks associated with data preperation
associated with Genome/Clinical files to be added to the Cancer Genome Browser
http://genome-cancer.ucsc.edu


===Most of these tools are still in developement===

Tools:

compileCancerData.py - Take collection of data and produce SQL for cancer genome browser
compileScan.py - Do checks on avalible data (doesn't produce actual SQL)

bed2probeMap.py	- Convert bed12 probe file to probeMap format	
	
	
getRefGene_hg18.sh - Download refgene program from Genome Browser database

extractFeatures.py, extractProbes.py, extractGenomic.py, extractSamples.py, extractClinical.py - 
	Extract data stored in previous mySQL schema ( to help with transition to cgData 1.0 )


tcgaAliquotSampleMap.sh - Produce sample map from TCGA sample report