Week 4: Parsing Files

This week, I discovered how to download files from the TCGA database, and explored their structure.

So this week, I downloaded 512 files relating to colorectal cancer (COAD in the TCGA database.) These were compressed into a Tar file, which opened into a directory tree that looked like this:


Each tiny blue dot is a folder, and inside each folder is one gzipped file (compressed). And each one of these files is a sample from a patient with gene, and its expression (from either a tumor sample or a healthy one.)

So my main issue has been to try and parse these files into a data matrix, ideally with sample-ids on the top and gene expression on the sides. So far, I’ve been able to compress these files into patient and samples relating to them because ideally, we want to look at gene expression in a healthy and tumor sample from the same patient. However, I haven’t been able to write the sample-ids with gene expression data into a file because of multiple bugs and errors. My goal for next week is to get these errors fixed.