Analysis examples for mSCAPE

Retrieve all samples that contain a particular taxa e.g. pseudomonas

This can be done through the CLI:

$ onyx filter mscape --field taxa_files.human_readable.icontains=pseudomonas --format csv

Or through the Python API:

import os
from onyx import OnyxConfig, OnyxClient, OnyxEnv, OnyxField

config = OnyxConfig(
    domain=os.environ[OnyxEnv.DOMAIN],
    token=os.environ[OnyxEnv.TOKEN],
)

with OnyxClient(config) as client:
    # Filter for read sets containing "pseudomonas"
    for metadata in client.query(
        "mscape",
        query=OnyxField(taxa_files__human_readable__icontains="pseudomonas"),
    ):
        # Do analysis here
        print("CLIMB ID:", metadata["climb_id"])
        print("Published date:", metadata["published_date"])

        # The query command by default does not return taxonomic information
        # To get this, we have to call the `get` method and retrieve the samples individually
        full_metadata = client.get("mscape", metadata["climb_id"])

        # Now we can inspect the taxonomic information for the readset
        print(
            "Number of binned reads:", len(full_metadata["taxa_files"])
        )  # etc. Do more analysis
        print("Pseudomonas taxa:")
        for taxa in full_metadata["taxa_files"]:
            if "pseudomonas" in taxa["human_readable"].lower():
                print("-", taxa["human_readable"])

Example output for this python script:

CLIMB ID: C-FE89BACF2D
Published date: 2024-02-28
Number of binned reads: 3
Pseudomonas taxa:
- Pseudomonas aeruginosa
- Pseudomonas aeruginosa PA7
CLIMB ID: C-470A57DCD0
Published date: 2024-02-28
Number of binned reads: 8
Pseudomonas taxa:
- Pseudomonas aeruginosa
- Pseudomonas aeruginosa PA7
CLIMB ID: C-FB67513BE0
Published date: 2024-02-28
Number of binned reads: 4
Pseudomonas taxa:
- Pseudomonas aeruginosa
CLIMB ID: C-E49EED98E4
Published date: 2024-02-28
Number of binned reads: 3
Pseudomonas taxa:
- Pseudomonas aeruginosa
- Pseudomonas aeruginosa PA7
...

Get a CSV distribution of all binned taxa present in the dataset

Through the CLI:

$ onyx filter mscape --summarise taxa_files.taxon_id,taxa_files.human_readable --format csv

Or through the Python API:

import os
from onyx import OnyxConfig, OnyxClient, OnyxEnv, OnyxField

config = OnyxConfig(
    domain=os.environ[OnyxEnv.DOMAIN],
    token=os.environ[OnyxEnv.TOKEN],
)

with OnyxClient(config) as client:
    for summary_data in client.query(
        "mscape",
        summarise=["taxa_files__taxon_id", "taxa_files__human_readable"],
    ):
        # Do analysis here
        print("Taxon ID:", summary_data["taxa_files__taxon_id"])
        print("Taxon name:", summary_data["taxa_files__human_readable"])
        print("Number of readsets present:", summary_data["count"])

Example output for this python script:

Taxon ID: 1304
Taxon name: Streptococcus salivarius
Number of readsets present: 22
Taxon ID: 1305
Taxon name: Streptococcus sanguinis
Number of readsets present: 9
Taxon ID: 1313
Taxon name: Streptococcus pneumoniae
Number of readsets present: 26
Taxon ID: 1318
Taxon name: Streptococcus parasanguinis
Number of readsets present: 42
Taxon ID: 1328
Taxon name: Streptococcus anginosus
Number of readsets present: 4
...