augur filter

Filter and subsample a sequence set.

usage: augur filter [-h] --metadata FILE [--sequences SEQUENCES]
                    [--sequence-index SEQUENCE_INDEX]
                    [--metadata-chunk-size METADATA_CHUNK_SIZE]
                    [--metadata-id-columns METADATA_ID_COLUMNS [METADATA_ID_COLUMNS ...]]
                    [--metadata-delimiters METADATA_DELIMITERS [METADATA_DELIMITERS ...]]
                    [--query QUERY]
                    [--query-columns QUERY_COLUMNS [QUERY_COLUMNS ...]]
                    [--min-date MIN_DATE] [--max-date MAX_DATE]
                    [--exclude-ambiguous-dates-by {any,day,month,year}]
                    [--exclude EXCLUDE [EXCLUDE ...]]
                    [--exclude-where EXCLUDE_WHERE [EXCLUDE_WHERE ...]]
                    [--exclude-all] [--include INCLUDE [INCLUDE ...]]
                    [--include-where INCLUDE_WHERE [INCLUDE_WHERE ...]]
                    [--min-length MIN_LENGTH] [--max-length MAX_LENGTH]
                    [--non-nucleotide] [--group-by GROUP_BY [GROUP_BY ...]]
                    [--sequences-per-group SEQUENCES_PER_GROUP | --subsample-max-sequences SUBSAMPLE_MAX_SEQUENCES]
                    [--probabilistic-sampling | --no-probabilistic-sampling]
                    [--priority PRIORITY] [--subsample-seed SUBSAMPLE_SEED]
                    [--output OUTPUT] [--output-metadata OUTPUT_METADATA]
                    [--output-strains OUTPUT_STRAINS]
                    [--output-log OUTPUT_LOG]
                    [--empty-output-reporting {error,warn,silent}]

inputs

metadata and sequences to be filtered

--metadata

sequence metadata

--sequences, -s

sequences in FASTA or VCF format

--sequence-index

sequence composition report generated by augur index. If not provided, an index will be created on the fly.

--metadata-chunk-size

maximum number of metadata records to read into memory at a time. Increasing this number can speed up filtering at the cost of more memory used.

Default: 100000

--metadata-id-columns

names of possible metadata columns containing identifier information, ordered by priority. Only one ID column will be inferred.

Default: (‘strain’, ‘name’)

--metadata-delimiters

delimiters to accept when reading a metadata file. Only one delimiter will be inferred.

Default: (‘,’, ‘t’)

metadata filters

filters to apply to metadata

--query
Filter samples by attribute.

Uses Pandas Dataframe querying, see https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#indexing-query for syntax. (e.g., –query “country == ‘Colombia’” or –query “(country == ‘USA’ & (division == ‘Washington’))”)

--query-columns

Use alongside –query to specify columns and data types in the format ‘column:type’, where type is one of (bool,float,str,int). Automatic type inference will be attempted on all unspecified columns used in the query. Example: region:str coverage:float.

--min-date

minimal cutoff for date, the cutoff date is inclusive; may be specified as: 1. an Augur-style numeric date with the year as the integer part (e.g. 2020.42) or 2. a date in ISO 8601 date format (i.e. YYYY-MM-DD) (e.g. ‘2020-06-04’) or 3. a backwards-looking relative date in ISO 8601 duration format with optional P prefix (e.g. ‘1W’, ‘P1W’)

--max-date

maximal cutoff for date, the cutoff date is inclusive; may be specified as: 1. an Augur-style numeric date with the year as the integer part (e.g. 2020.42) or 2. a date in ISO 8601 date format (i.e. YYYY-MM-DD) (e.g. ‘2020-06-04’) or 3. a backwards-looking relative date in ISO 8601 duration format with optional P prefix (e.g. ‘1W’, ‘P1W’)

--exclude-ambiguous-dates-by

Possible choices: any, day, month, year

Exclude ambiguous dates by day (e.g., 2020-09-XX), month (e.g., 2020-XX-XX), year (e.g., 200X-10-01), or any date fields. An ambiguous year makes the corresponding month and day ambiguous, too, even if those fields have unambiguous values (e.g., “201X-10-01”). Similarly, an ambiguous month makes the corresponding day ambiguous (e.g., “2010-XX-01”).

--exclude

file(s) with list of strains to exclude

--exclude-where

Exclude samples matching these conditions. Ex: “host=rat” or “host!=rat”. Multiple values are processed as OR (matching any of those specified will be excluded), not AND

--exclude-all

exclude all strains by default. Use this with the include arguments to select a specific subset of strains.

Default: False

--include

file(s) with list of strains to include regardless of priorities, subsampling, or absence of an entry in –sequences.

--include-where

Include samples with these values. ex: host=rat. Multiple values are processed as OR (having any of those specified will be included), not AND. This rule is applied last and ensures any strains matching these rules will be included regardless of priorities, subsampling, or absence of an entry in –sequences.

sequence filters

filters to apply to sequence data

--min-length

minimal length of the sequences, only counting standard nucleotide characters A, C, G, or T (case-insensitive)

--max-length

maximum length of the sequences, only counting standard nucleotide characters A, C, G, or T (case-insensitive)

--non-nucleotide

exclude sequences that contain illegal characters

Default: False

subsampling

options to subsample filtered data

--group-by

categories with respect to subsample. Notes: (1) Grouping by [‘month’, ‘week’, ‘year’] is only supported when there is a ‘date’ column in the metadata. (2) ‘week’ uses the ISO week numbering system, where a week starts on a Monday and ends on a Sunday. (3) ‘month’ and ‘week’ grouping cannot be used together. (4) Custom columns [‘month’, ‘week’, ‘year’] in the metadata are ignored for grouping. Please rename them if you want to use their values for grouping.

--sequences-per-group

subsample to no more than this number of sequences per category

--subsample-max-sequences

subsample to no more than this number of sequences; can be used without the group_by argument

--probabilistic-sampling

Allow probabilistic sampling during subsampling. This is useful when there are more groups than requested sequences. This option only applies when –subsample-max-sequences is provided.

Default: True

--no-probabilistic-sampling

Default: True

--priority
tab-delimited file with list of priority scores for strains (e.g., “<strain>t<priority>”) and no header.

When scores are provided, Augur converts scores to floating point values, sorts strains within each subsampling group from highest to lowest priority, and selects the top N strains per group where N is the calculated or requested number of strains per group. Higher numbers indicate higher priority. Since priorities represent relative values between strains, these values can be arbitrary.

--subsample-seed

random number generator seed to allow reproducible subsampling (with same input data).

outputs

options related to outputs, at least one of the possible representations of filtered data (–output, –output-metadata, –output-strains) is required

--output, --output-sequences, -o

filtered sequences in FASTA format

--output-metadata

metadata for strains that passed filters

--output-strains

list of strains that passed filters (no header)

--output-log

tab-delimited file with one row for each filtered strain and the reason it was filtered. Keyword arguments used for a given filter are reported in JSON format in a kwargs column.

--empty-output-reporting

Possible choices: error, warn, silent

How should empty outputs be reported when no strains pass filtering and/or subsampling.

Default: error

Guides

See Filtering and Subsampling.