metagenome-atlas/atlas: Use parquet and pyfastx to handle large gene catalogs
- Silas Kieser
- Joe Brown
- Sean M. Colby
- Richard Allen White III
- Jackson M. Tsuji
- Yan Hui
- Cedric Midoux
- Chris Overall
- Mattias de Hollander
- C. Titus Brown
- Christopher Bottoms
- Colin Brislawn
- Roshni Biswas
- Vladimir Mikryukov
- Jie Zhu
- wangzc
Publication date
August 2022
DOIAbstract
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.
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