The general command line for running jfastafunk is:
jfastafunk <command> [options]
| command | description |
|---|---|
annotate |
Take data fields from a metadata file and apply to the sequence headers. |
compress |
Compress to functionally identical sequences. |
extract |
Extract sequences from a list or based on metadata. |
remove |
Remove sequences from a list or based on metadata. |
-h / --help List the available options and stop. Combine with a command to get help for that command.
--version Print the version number and stop.
-v / --verbose Print extended information about analysis performed.
These options specify the input and output files and are used by most of the commands.
-i / --input <filename> Specify the input file.
-m / --metadata <filename> Specify a metadata table in CSV or TSV format where required.
-t / --taxa <filename> Specify a list of taxa in CSV format or as a tree where required.
-o / --output <output_path> Output filename or path to a directory if multiple output files will be produced.
-d / --output-metadata <file> Output a metadata file to match the output file.
-p / --prefix <file_prefix> Output file prefix when multiple output files are produced.
These options are used by functions where a metadata file (in CSV or TSV format) is provided and the rows in the table are matched to the sequences using unique IDs or strings. These link a column in the metadata table (using the --id-column option specifying the column name) to the label/header of the sequences in the FASTA file. Optionally this link can be made to a specific 'field' in the label using the --id-field option and the number of the field. Fields in a sequence label are strings (i.e., accessions, locations, dates) separated by a delimiter character (by default it uses the bar | character).
-c / --id-column <column name> Metadata column to use to match labels with the row in the metadata table (default first column)
-n / --id-field <field number> The label field to use to match metadata rows indexed from 1 (default = whole label)
--field-delimiter <delimiter> The delimiter used to specify fields in the labels (default |)
--ignore-missing Ignore any sequences that don't have a match in the annotations table (default: stop and report missing metadata).
This command adds information from the metadata file into the sequence labels as fields separated by a character (by default the bar character, | ). A match between the metadata row and the sequence label is made using an index column (by default the first column) and a field in the sequence label (by default the entire label).
--annotate-description Put the annotations in the sequence description rather than appending to the name. A sequence description is after the sequence label separated by a space (default false).
--label-fields <columns> A list of metadata columns to add as label fields.
--default-value <value> The default value to use for each field if the index is not found in the metadata.
-r / --replace Replace the entire existing label rather than appending (default: append).
Example:
jfastafunk annotate -i sequences.fasta -m metadata.csv --index-column sample --index-field 1 --label-fields country date -o annotated.fasta
This would match the value in the metadata column called sample with the first field in the FASTA sequence label and then append the values for country and date to the label.
This would result in a label like this:
>seq1234|Scotland|1972-02-19
ATGATGCCGAGCGAGA...
This command de-duplicates sequences that have matching labels or that have the same value in one or more columns of the metadata table.
This command extracts sequences where the label fields or metadata columns match specified values. Can also be used to extract all the sequences that match a set of taxa (either a list in a file or in a tree).
--match <columns> A list of metadata columns and regex values to match to. Example:
country="Scotland|England"
Example:
jfastafunk extract -i sequences.fasta -m metadata.csv --match date="2024" --output-metadata extracted.csv -o extracted.fasta
This would match the sequences with the metadata rows using the first columns and the complete FASTA sequence label and then write only those sequences that had 2024 in the date column. It would also create a new version of the metadata table that only had rows for the extracted sequences.