mgnify-extract

This library extracts Darwin Core datasets from MGnify. API documentation at https://iobis.github.io/mgnify-extract.

Usage

Find studies:

from mgnifyextract.studies import find_studies

filters = {
    "lineage": "root:Environmental:Aquatic:Marine",
    "search": "Tara"
}
studies = find_studies(filters, max_results=1)

Fetching samples, runs, analyses, and downloads:

from mgnifyextract.studies import get_study

study = get_study("MGYS00000462")
# <Study https://www.ebi.ac.uk/metagenomics/studies/MGYS00000462>

samples = study.get_samples()
# [<Sample https://www.ebi.ac.uk/metagenomics/samples/ERS667567>, <Sample https://www.ebi.ac.uk/metagenomics/samples/ERS667569>, <Sample https://www.ebi.ac.uk/metagenomics/samples/ERS667570>, ...]

runs = samples[0].get_runs()
# [<Run https://www.ebi.ac.uk/metagenomics/runs/ERR867642>, <Run https://www.ebi.ac.uk/metagenomics/runs/ERR867641>, <Run https://www.ebi.ac.uk/metagenomics/runs/ERR770958>]

analyses = runs[0].get_analyses()
# [<Analysis https://www.ebi.ac.uk/metagenomics/analyses/MGYA00593805>, <Analysis https://www.ebi.ac.uk/metagenomics/analyses/MGYA00135741>]

downloads = analyses[0].get_downloads()
# [<FastaDownload Sequence data https://www.ebi.ac.uk/metagenomics/api/v1/analyses/MGYA00593805/file/ERR867642_MERGED_FASTQ.fasta.gz?format=json>, <FastaDownload Taxonomic analysis SSU rRNA https://www.ebi.ac.uk/metagenomics/api/v1/analyses/MGYA00593805/file/ERR867642_MERGED_FASTQ_SSU.fasta.gz?format=json>, <MseqDownload Taxonomic analysis SSU rRNA https://www.ebi.ac.uk/metagenomics/api/v1/analyses/MGYA00593805/file/ERR867642_MERGED_FASTQ_SSU_MAPSeq.mseq.gz?format=json>, <TsvDownload Taxonomic analysis SSU rRNA https://www.ebi.ac.uk/metagenomics/api/v1/analyses/MGYA00593805/file/ERR867642_MERGED_FASTQ_SSU_OTU.tsv?format=json>, <Hdf5BiomDownload Taxonomic analysis SSU rRNA https://www.ebi.ac.uk/metagenomics/api/v1/analyses/MGYA00593805/file/ERR867642_MERGED_FASTQ_SSU_OTU_TABLE_HDF5.biom?format=json>, <JsonBiomDownload Taxonomic analysis SSU rRNA https://www.ebi.ac.uk/metagenomics/api/v1/analyses/MGYA00593805/file/ERR867642_MERGED_FASTQ_SSU_OTU_TABLE_JSON.biom?format=json>]

Generating Darwin Core tables:

from mgnifyextract.studies import get_superstudy_studies
from mgnifyextract.dwc import study_to_dwc

study = get_superstudy_studies("atlanteco")[0]
# <Study https://www.ebi.ac.uk/metagenomics/studies/MGYS00005780>

occ, dna = study_to_dwc(study)

Run scripts

PYTHONPATH=. python scripts/develop.py

Run module

python -m mgnifyextract