OTUs

Delete an OTU

Deletes and OTU and its associated isolates and sequences.

Request

delete
/otus/{otu_id}

Get an OTU

Fetches the details of an OTU.

A FASTA file containing all sequences in the OTU can be downloaded by appending .fa to the path.

Errors

StatusDescription
403
404

Request

get
/otus/{otu_id}

Response

{
  "status": "200"
}

Update an OTU

Checks to make sure the supplied OTU name and abbreviation don't already exist in the parent reference.

Parameters

Name Type Required Description
abbreviation string false
name string false
schema array false

Errors

StatusDescription
400
403
404

Request

patch
/otus/{otu_id}

Response

{
  "status": "200"
}

List isolates

Lists all the isolates and sequences for an OTU.

Request

get
/otus/{otu_id}/isolates

Create an isolate

Creates an isolate on the OTU specified by otu_id.

Parameters

Name Type Required Description
default boolean false
source_name string false
source_type string false

Errors

StatusDescription
401
404

Request

post
/otus/{otu_id}/isolates

Response

{
  "status": "201"
}

Delete an isolate

Deletes an isolate using its 'otu id' and 'isolate id'.

Request

delete
/otus/{otu_id}/isolates/{isolate_id}

Get an isolate

Fetches the details of an isolate.

A FASTA file containing all sequences in the isolate can be downloaded by appending .fa to the path.

Errors

StatusDescription
404

Request

get
/otus/{otu_id}/isolates/{isolate_id}

Response

{
  "status": "200"
}

Update an isolate

Updates an isolate using 'otu_id' and 'isolate_id'.

Parameters

Name Type Required Description
source_name string false
source_type string false

Errors

StatusDescription
401
404

Request

patch
/otus/{otu_id}/isolates/{isolate_id}

Response

{
  "status": "200"
}

List sequences

Lists the sequences for an isolate.

Errors

StatusDescription
401
403
404

Request

get
/otus/{otu_id}/isolates/{isolate_id}/sequences

Response

{
  "status": "200"
}

Create a sequence

Creates a new sequence for an isolate identified by otu_id and isolate_id.

Parameters

Name Type Required Description
accession string true
definition string true
host string false
segment string false
sequence string true
target string false

Errors

StatusDescription
400
403
404

Request

post
/otus/{otu_id}/isolates/{isolate_id}/sequences

Response

{
  "status": "201"
}

Delete a sequence

Deletes the specified sequence.

Request

delete
/otus/{otu_id}/isolates/{isolate_id}/sequences/{sequence_id}

Get a sequence

Fetches the details for a sequence.

A FASTA file containing the nucelotide sequence can be downloaded by appending .fa to the path.

Request

get
/otus/{otu_id}/isolates/{isolate_id}/sequences/{sequence_id}

Update a sequence

Updates a sequence using its 'otu id', 'isolate id' and 'sequence id'.

Parameters

Name Type Required Description
accession string false
definition string false
host string false
segment string false
sequence string false
target string false

Errors

StatusDescription
400
401
403
404

Request

patch
/otus/{otu_id}/isolates/{isolate_id}/sequences/{sequence_id}

Response

{
  "status": "200"
}