domainator hmmer_report
Tabulate properties of each HMM profile.
Writes record-wise information from hmm files into tab-separated or html tables
Amino acid, DNA, and RNA profiles are all supported; use --alphabet to report which
alphabet each profile uses.
Give at least one of these outputs: --tsv_out, --html_out, --json_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 | hmm filenames. Use - to read standard input. |
-o, --tsv_out |
FILE | Write the table to this tab-separated file. Use - for standard output. | |
--html_out |
FILE | Write the table in html format to this file. Use - for standard output. | |
--json_out |
FILE | Write streaming NDJSON (one compact JSON object per profile) to this file. Use - for standard output. | |
--html_max_height |
INTEGER | Max height in pixels to set the html output to. | |
--column_names |
STRING ... | If supplied, then this list will be used instead of the default column names. | |
--columns |
columns... | The columns to report, in order. A column with arguments takes them after ':', as in 'qualifier:CDS:product'. Can be given more than once. |
Columns
| Column | Description |
|---|---|
source |
the name of the hmm file. |
acc |
the profile's accession. |
desc |
the profile's description. |
length |
the length of the profile (the number of nodes). |
consensus |
the profile's consensus residue line, if set. |
alphabet |
the profile's alphabet (amino, DNA, or RNA). |
append:name:type:value |
a column with this name and type (str, int or float) holding this value in every row. |
Every command also takes --config FILE (options from a JSON or YAML file, keyed by option name) and --print_config.