Run microbetag from Python

One may use the API routes described through Python. For example, to get the microbetagDB genomes related species with NCBI Taxonomy id 853:

import requests
url = "https://msysbio.gbiomed.kuleuven.be/ncbiTaxId-to-genomeId/853"
r = requests.get(url)
r.status_code
200
r.json()
{"537007": ["GCA_002222595.2"]}

Furthermore, one may run microbetag directly and not through the CytoscapeApp by simply converting their abundance table or co-occurrence network in a JSON object. They would also need to provide the following arguments as part of the JSON obect:

arguments_list = ["input_category", "taxonomy", "phenDB", "faprotax", "pathway_complement", "seed_scores"]

Here is an example using an ASV abundance table as input, asking for all microbetag annotations supported:

import requests
import json

# Init a json object
json_object = {}

# Load the abundance table and after removing any blanks load it as lines in the json object
data = open("my_abundance_table.tsv","r")
data = data.readlines()
data = [line.rstrip("\n").split("\t") for line in data]
json_object["data"] = data

# Likewise, in case you already have a network of your own 
edgelist =  open("edgelist.csv","r")
edgelist = edgelist.readlines()
edgelist = [line.rstrip("\n").split("\t") for line in edgelist]
json_object["network"] = edgelist


# Make a dictionary with your arguments settings
args = {
  "taxonomy":"Silva", 
  "delimiter": ";", 
  "faprotax": True, 
  "phenDB": True, 
  "pathway_complement": True,
  "seed_scores": True,
  "manta": False,
} 
json_object["inputParameters"] = args

# Load your metadata file like in the data case; if no metadata you can skip this
# json_object["metadata"] =

# Set the url to the microbetag server
url = "https://msysbio.gbiomed.kuleuven.be/upload-abundance-table-dev"

# Run microbetag
r = requests.post(url, json = json_object)

# Save your annotated network to a json file that cytoscape can load
response_dict = r.json()
with open('new_microbetag.cx', 'w') as f:
	json.dump(response_dict, f, indent=4, sort_keys=True)

Apparently, the my_abundance_table.tsv and the edgelist.csv files can be in any format initially. Yet, they need to be converted in a way so eventually what you send to the microbetag server is in the form of data and network in the above chunk. These look like this:

>>> data
[
  ['seqId', 'sample1', 'sample2', 'taxonomy'],
  ['bin_100', '77', '1', 'd__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Terrimonas;s__Terrimonas ferruginea'], ...
]
>>>edgelist
[
  ['nodeA', 'nodeB', 'weight'], 
  ['bin_45', 'bin_28', '0.471'], ...
]

POSSIBLE ARGUMENT’S VALUES

input_category: [abundance_table | network]

taxonomy: [GTDB | Silva | microbetag_prep | other]

phenDB, faprotax, pathway_complement, seed_scores: [True | False], get_children

You arguments dictionary needs to include all the arguments mentioned above. If any is not provided , microbetag will eventually fail and won’t return an annotated network.

Syntax common error: make sure you do not have a / in the end of the url. If so, microbetag will never start.