domainator clean_sequences
Clean sequence names and residues, and filter out sequences with non-canonical residues.
Clean and filter sequences in genbank or fasta files
This module provides functionality to:
- Clean sequence names for compatibility with newick format
- Deduplicate sequence names to ensure uniqueness
- Strip non-canonical residues from sequence ends
- Filter out sequences containing non-canonical residues
Give at least one of these outputs: --genbank_out, --fasta_out. - as an input or output means standard input or output, where the option says it is allowed.
| Option | Value | Default | Description |
|---|---|---|---|
-v, --verbose |
show debug output, and a traceback for errors. | ||
-q, --quiet |
show errors only: no progress messages or warnings. | ||
-i, --input |
FILE ... | required | Names of input genbank files. Use - to read standard input. |
--alphabet |
{nucleotide,protein} | protein | Whether the sequences in FASTA inputs are protein or nucleotide. GenBank records declare their own molecule type. |
-o, --genbank_out |
FILE | Write the records to this GenBank file. Use - for standard output. | |
--fasta_out |
FILE | Write the records to this FASTA file. Use - for standard output. | |
--clean_name |
if true then make the name compatible with newick format. | ||
--deduplicate_names |
if true then rename sequences such that output sequences have unique names. | ||
--strip |
if true then strip non-canonical residues or nucleotides from the ends of sequences (depending on input type). Including * characters. | ||
--filter_by_aa |
if true then throw out sequences containing non-canonical residues or nucleotides (depending on input type). Including * characters. (applied after strip) | ||
--log_out |
FILE | Write the cleaning statistics to this file. If not supplied, writes them to stderr. |
Every command also takes --config FILE (options from a JSON or YAML file, keyed by option name) and --print_config.