augur.filter module¶
Filter and subsample a sequence set.
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augur.filter.
filter_by_query
(sequences, metadata_file, query)¶ Filter a set of sequences using Pandas DataFrame querying against the metadata file.
- Parameters
sequences (list[str]) – List of sequence names to filter
metadata_file (str) – Path to the metadata associated wtih the sequences
query (str) – Query string for the dataframe.
- Returns
List of sequence names that match the given query
- Return type
list[str]
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augur.filter.
read_priority_scores
(fname)¶
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augur.filter.
read_vcf
(filename)¶
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augur.filter.
register_arguments
(parser)¶
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augur.filter.
run
(args)¶ filter and subsample a set of sequences into an analysis set
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augur.filter.
write_vcf
(input_filename, output_filename, dropped_samps)¶