domainator select_by_coord
Extract contig regions listed in a coordinate table.
Extract contig regions using explicit coordinate ranges.
Reads a labeled coordinate table into memory, then iterates through the input
contigs and extracts one region for each matching row.
Required table columns:
contig, start, end
Optional table columns:
strand, file
Coordinates are 1-based and inclusive.
If end < start, the region is assumed to wrap around the origin of a circular
contig. The same coordinates on a linear contig raise an exception.
Extracted regions are named like those of the other Domainator tools
(see utils.region_id): contig_first:last, where first and last are the
coordinates of the first and last bases of the region as written, followed by
'rc' for reverse-strand regions. For example, start 10, end 20, strand - is
named contig_20:10rc. Whole contigs keep their names (contig_rc if reverse).
If a file column is supplied, it must contain basenames only (with extension).
Rows without a file value match any input file.
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. |
-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. | |
--coords |
FILE | required | labeled coordinate table with columns contig, start, end, strand (optional), file (optional). |
Every command also takes --config FILE (options from a JSON or YAML file, keyed by option name) and --print_config.