domainator summary_report
Summarize the domain and taxonomy content of a dataset.
From a domainator-annotated genbank file, calculates contig stats and domain frequency stats
Give at least one of these outputs: --text_out, --html_out, --json_out, --domains_tsv_out, --co_occurrence_fraction_out, --co_occurrence_count_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 | name of input genbank files. Use - to read standard input. |
-o, --text_out |
FILE | Write the report as text to this file. Use - for standard output. | |
--html_out |
FILE | Write the report as html to this file. Use - for standard output. | |
--json_out |
FILE | Write the full summary as a single compact JSON object to this file. Use - for standard output. | |
--domains_tsv_out |
FILE | Write a tab-separated table of domain frequencies to this file. Headers are: domain, database, count, description, avg score. | |
--co_occurrence_fraction_out |
FILE | Write a dense text matrix of domain co-occurrence frequencies to this file. Every row is a domain, the values are the fraction of contigs containing the row-domain that also include the column-domain (so the matrix is asymmetric). | |
--co_occurrence_count_out |
FILE | Write a dense text matrix of domain co-occurrence frequencies to this file. Every row is a domain, the values are the number of contigs containing both the row-domain and the column-domain (so the matrix is symmetric). | |
--taxonomy |
Write a summary of the taxonomic origins of the contigs. | ||
--taxonomy_update |
If taxonomy database exists, check it against the version on the ncbi server and update if there is a newer version. | ||
--ncbi_taxonomy_path |
DIR | /tmp/ncbi_taxonomy_sean | Path to NCBI taxonomy database directory. Will be created and downloaded if it does not exist. |
--contigs |
STRING ... | Only consider contigs with these names. | |
--contigs_file |
FILE | text file containing names of contigs to select. | |
--domains |
STRING ... | calculate distance graphs for domains with these names | |
--domains_file |
FILE | text file containing names of domains to calculate distance graphs for. | |
--databases |
STRING ... | Ignore domain annotations not from these databases. default: consider all databases. | |
--partial |
{include,exclude,only} | include | Which CDSs/proteins to count, by fragment status. include: all. exclude: skip fragments. only: only fragments. A CDS is a fragment if its location has '<' or '>', or it has a /partial qualifier. A protein record is a fragment if it has a UniProt ' (Fragment)' or MGnify 'FL=0' header, a 'Flags: Fragment' definition or NON_TER features (UniProt text entries), or a CDS/Protein feature with '<' or '>' spanning it. Protein records that are filtered out are skipped; on nucleotide contigs, filtered CDSs and their domains are not counted, but the contig is. |
Every command also takes --config FILE (options from a JSON or YAML file, keyed by option name) and --print_config.