Download the Sample Data Set

First, if you haven’t installed the package, you can do so using PyPI (in the terminal):

#!pip install metadex
import metadex

Get Study Information from MG-RAST

MG-RAST assigns each metagenome a metagenome ID (mgm...). For each metagenome you would like to include in your study, you will need: - metagenome ID - corresponding assigned group - corresponding assigned sample ID (within the group can be 1, 2, 3; or something more specfic)

Download Gene Counts Matrix from MG-RAST

1. Go to Analyze section of MG-RAST
2. Select the following metagenomes: - mgm739968.3 - mgm739969.3 - mgm739970.3 - mgm739971.3
3. Select matrix
4. Export to CSV (tab-separated CSV)

Getting Annotations from MG-RAST

Based on the information above, we can download the full counts (the main information) directly via API:

metadex.get_all_async('lagoon study', {'mgm4739968.3':'nador_lagoon', 'mgm4739969.3':'oualidia_lagoon', 'mgm4739970.3': 'oualidia_lagoon', 'mgm4739971.3':'nador_lagoon'}, 'RefSeq', evalue=5, identity=60, length=15)

First MetaDEx creates a directory named ‘lagoon study’ in which it downloads the annotations for each metagenome (e.g. mgm4739968.3) to corresponding tab- separated files named for the group and ID (e.g. nador_lagoon_1_counts.tsv).

When this step is complete the lagoon study directory should look as follows:

lagoon study - nador_1.tsv - nador_2.tsv - oualidia_1.tsv - oualidia_2.tsv