Published August 5, 2022
| Version v2.11.0
Software
Open
metagenome-atlas/atlas: Use parquet and pyfastx to handle large gene catalogs
Creators
- 1. @pnnl
- 2. University of Copenhagen
- 3. @inra-migale
- 4. Netherlands Institute of Ecology (NIOO-KNAW)
- 5. University of California, Davis
- 6. Oklahoma Medical Research Foundation
- 7. @PNNL
- 8. UT (EE)
Description
What's Changed
- Make atlas handle large gene catalogs using parquet and pyfastx (Fix #515)
parquet files can be opened in python with
import pandas as pd
coverage = pd.read_parquet("working_dir/Genecatalog/counts/median_coverage.parquet")
coverage.set_index("GeneNr", inplace=True)
and in R it should be something like:
arrow::read_parquet("working_dir/Genecatalog/counts/median_coverage.parquet")
Full Changelog: https://github.com/metagenome-atlas/atlas/compare/v2.10.0...v2.11.0
Files
metagenome-atlas/atlas-v2.11.0.zip
Files
(1.5 MB)
| Name | Size | Download all |
|---|---|---|
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md5:fe7d529cb26e8c22b3c682e70ad71d1c
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1.5 MB | Preview Download |
Additional details
Related works
- Is supplement to
- https://github.com/metagenome-atlas/atlas/tree/v2.11.0 (URL)