While not the most popular means of storing data, there are instances where data is stored in the XML file format. The TCGA project is one such group that keeps a record of samples and analysis information in this format. It can be difficult to extract data from these files without the appropriate tools. In some cases a simple grep command can be used, but even then the output usually needs to be cleaned. Luckily, Python has some packages that are aid in parsing XML files so that the desired data can be extracted. The library I found most useful was ElementTree. This package combined with the urllib2 package enables one to download an XML file remotely from the internet, parse the XML file, and extract the desired information from the data stored within the XML file. Below is an example Python script that downloads an XML description file from TCGA (link) and then places each extracted element into a Python dictionary object. Of course this could be easily modified for your particular application of interest, but at least it provides a simple backbone to easily build other scripts off of.
Below is the expected output:
Welcome to the Genome Toolbox! I am glad you navigated to the blog and hope you find the contents useful and insightful for your genomic needs. If you find any of the entries particularly helpful, be sure to click the +1 button on the bottom of the post and share with your colleagues. Your input is encouraged, so if you have comments or are aware of more efficient tools not included in a post, I would love to hear from you. Enjoy your time browsing through the Toolbox.