A new look at the Amazon Continuum Metagenomes project

Author: Kai Blumberg

Email: [email protected]

Script: amazon_xml_parser.py

A script to parse the Amazon Continuum Metagenomes project's metadata from an xml file. The script parses all the samples into a list of dictionaries, each of which contains all metadata for a sample as key value pairs in the dictionaries.

After parsing the metadata, the script plots depth profiles of biogeochemical parameters such as dissolved oxygen and dissolved inorganic carbon.

The xml file was obtained form the NCBI National center for Biotechnological information bioproject 237344 and clicking on send to chose file then chose select the Format as Full XML (text) the click Create File.

XML parsing script based on the example provided by Ken Youens-Clark from the University of Arizona Biosystems analytics course, from lecture 9 as well as the xml.etree.ElementTree documentation.

In order to run the script the user will need to have matplotlib installed. If using an anaconda environment simply run conda install -c conda-forge matplotlib.

Run the program by calling:

./amazon_xml_parser.py biosample_result.xml

The program should generate the output files: Dissolved_Oxygen_profile.png and Dissolved_Inorganic_carbon_profile.png

Test that the program has executed correctly by running: make test