augur.filter module¶
Filter and subsample a sequence set.
-
exception
augur.filter.
TooManyGroupsError
(msg)¶ Bases:
ValueError
-
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]
-
augur.filter.
numeric_date
(date)¶ Converts the given date string to a
float
.date may be given as a number (a float) with year as the integer part, or in the YYYY-MM-DD (ISO 8601) syntax.
>>> numeric_date("2020.42") 2020.42 >>> numeric_date("2020-06-04") 2020.42486...
-
augur.filter.
read_priority_scores
(fname)¶
-
augur.filter.
read_vcf
(filename)¶
-
augur.filter.
register_arguments
(parser)¶
-
augur.filter.
run
(args)¶ filter and subsample a set of sequences into an analysis set
-
augur.filter.
write_vcf
(input_filename, output_filename, dropped_samps)¶