uBiome is offering the much needed service of telling us the make up of our microbiome. They provide friendly user interfaces to review the results. Despite beautiful charts and comparison tools one of the limitations of uBiome’s web services is that you cannot compare three or more samples at once. This is a bummer for biohackers who are regularly submitting samples and want to see their changes over months and years. uBiome has posted some python tools through github to allow users to go further. Special thanks to Richard Sprague for contributing to so many microbiome tools on GitHub and a Microbiome Hackers Guide.
In order to merge three or more ubiome results we will need to do the following five steps:
download uBiome JSON file results
install the uBiome python library
create a python script to merge the files
view the results on the command line
Download uBiome JSON file results:
Login to uBiome
Click on Advanced
Download Taxonomy JSON
repeat for each date results are available for
Install the ubiome python library:
$ pip install ubiome
$ pip install csvkit
$ cat ubiome-multi-merge.py
Create a python script to merge the files:
from ubiome import *
f1 = UbiomeSample(“2016-11-21”)
f2 = UbiomeSample(“2017-04-01”)
f3 = UbiomeSample(“2018-01-29”)
m = UbiomeMultiSample(f1)
Run the merge script and view the results:
$ csvsort -c 3 -r merged-files.csv | csvlook
Once you have a merged the CSV file you could of course use Google Sheets to view and sort the columns. My preference is for the command line so I use csvkit to compare my three years of microbiome results. The shifts I’ve seen over two years of testing are huge.
8-6-2021 (August 6, 2021) is the Snakiest day of the year and it’s also this year’s CircuitPython Day! The day highlights all things CircuitPython and Python on Hardware. See you there!
Stop breadboarding and soldering – start making immediately! Adafruit’s Circuit Playground is jam-packed with LEDs, sensors, buttons, alligator clip pads and more. Build projects with Circuit Playground in a few minutes with the drag-and-drop MakeCode programming site, learn computer science using the CS Discoveries class on code.org, jump into CircuitPython to learn Python and hardware together, TinyGO, or even use the Arduino IDE. Circuit Playground Express is the newest and best Circuit Playground board, with support for CircuitPython, MakeCode, and Arduino. It has a powerful processor, 10 NeoPixels, mini speaker, InfraRed receive and transmit, two buttons, a switch, 14 alligator clip pads, and lots of sensors: capacitive touch, IR proximity, temperature, light, motion and sound. A whole wide world of electronics and coding is waiting for you, and it fits in the palm of your hand.