ranchero 0.1.0rc20

Ranchero: metadata wrangling for bioinformatics

Ranchero

Is your mycobacterial metadata a mess? Grab the M. bovis by the horns with Ranchero.

Ranchero is a Python solution to the dozens of different metadata formats used in genomic datasets. While it is specifically focused on NCBI's collection of Mycobacterium tuberculosis complex metadata, it still has utility for other organisms. For information on what Ranchero considers "a sample" and the like, see ./docs/data_structure.md. For information on how to configure Ranchero, see .docs/configuration.md.

Features

• Input a TSV/JSON/CSV of new samples and their metadata into a dataframe
• Merge columns of similar data types into a single column, filling in nulls/empty values as you go
• Input a TSV of metadata to "inject" into an existing dataframe, optionally overriding metadata already present
• Flatten all of those "missing" and "Not Applicable" strings into proper null values
• Convert countries into three-letter country codes per ISO 3166
• Convert dates to YYYY-MM-DD format into an ISO 8601-like format -- missing months/days are denoted as NN.
• Convert common host animal names to a standarized Genus species "common name" format
• (tuberculosis only) Convert old-school strain names to the modern lineage system

Dependencies

• Python 3.11-ish (3.9+ should be okay)
• pandas >= 2.0.0
• pyarrow, even if not working with Apache Arrow datasets
• polars for Python == 1.27.0
• tqdm
• xmltodict for working with Enterz Direct files

Supported inputs

Platform	Expected format	Ranchero function
BigQuery	newline-delimited JSONL†	from_bigquery()
Enterz Direct (efetch)	XML‡	from_efetch()
NCBI SRA web search	XML‡	from_efetch()
Excel/LibreOffice	TSV (XLSX not supported)	from_tsv()
Google Sheets	TSV	from_tsv()
NCBI Run Selector	CSV	from_run_selector()
basically anything else	TSV	from_tsv()

^† BQ typically outputs JSONs in a format polars does not like; from_bigquery() will fix it on the fly. ^‡ efetch typically outputs an invalid XML; from_efetch() will fix it on the fly. However, note that only -db sra -format native -mode xml and output from NCBI SRA web search is supported.