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