HMMs
Find HMMs
Lists profile hidden Markov model (HMM) annotations that are used in Virtool for novel virus prediction.
Providing a search term will return HMMs with full or partial matches in the
names attribute.
Each HMM annotation is generated from numerous public viral protein sequences.
The top three most common names in the protein records are combined into the
names attribute.
Request
get
/hmms
Response
{
"status": "200"
}Get HMM status
Lists the installation status of the HMM data. Contains the following fields:
| Field | Type | Description |
|---|---|---|
errors |
array[string] | An array of any errors in the HMM data |
installed |
object | A description of the currently installed HMM release |
task.id |
integer | The id the task responsible for installing the HMM data |
release |
object | A description of the latest available release |
Installed HMM data cannot currently be updated.
Request
get
/hmms/status
Response
{
"status": "200"
}Get the latest HMM release
Fetches the latest release for the HMM data.
Errors
| Status | Description |
|---|---|
| 502 | Cannot reach GitHub |
Request
get
/hmms/status/release
Response
{
"status": "200"
}List updates
Lists all updates applied to the HMM collection.
Request
get
/hmms/status/updates
Response
{
"status": "200"
}Install HMMs
Installs the latest official HMM database from GitHub.
Errors
| Status | Description |
|---|---|
| 400 | Target release does not exist |
| 403 | Not permitted |
Request
post
/hmms/status/updates
Response
{
"status": "201"
}Get an HMM
Fetches the details for an HMM annotation.
Errors
| Status | Description |
|---|---|
| 404 | Not found |
Request
get
/hmms/{hmm_id}
Response
{
"status": "200"
}