Parsers

How it works?

from moonstone.parsers import YourFavouriteParser

parser = YourFavouriteParser("/path/to/the/file")
df = parser.dataframe

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Counts

Simple Counts

GeneCountsParser(*args, **kwargs)	Common way of representing gene counts per sample in a matrix.
Picrust2PathwaysParser(*args, **kwargs)	Predicted sample pathway abundances output file from Picrust2.

Taxonomy Counts

SunbeamKraken2Parser(*args, **kwargs)	Parse output from Kraken2 merge table from Sunbeam pipeline.
Metaphlan2Parser(*args[, analysis_type])	Parse output from Metaphlan2 merged table.
Metaphlan3Parser(*args[, analysis_type])	Parse output from Metaphlan3 merged table.
Qiime2Parser(*args, **kwargs)	Parse output csv data obtained by Qiime2.

Metadata

MetadataParser(*args[, index_col, …])	Parse metadata file and allows to apply transformations on them (cleaning…).
YAMLBasedMetadataParser(metadata_file_path, …)	Metadata Parser with operations configured in a YAML file.