API for programmatic remote BLAST to SequenceServer instances

SequenceServer Cloud provides dedicated secure servers to BLAST your data and visualize results. Sometimes, you just want to do this programmatically.

Here, we have examples for Python and the unix command-line. The same principles could be carried over to other languages such as R, Go, or Java.

Python API for remote BLAST

This repository provides a lightweight Python API wrapper to SequenceServer Cloud users to execute BLAST queries against DBs on their SequenceServer Cloud instance.

Here’s an example of how it works:

from sequenceserver.sequenceserver_api import SequenceServerApi
import os

base_url = os.environ.get("SEQUENCESERVER_INSTANCE_URL", "https://YOURINSTANCE.sequenceserver.com")
api_token = os.environ.get("SEQUENCESERVER_API_TOKEN", "REDACTED_OBTAIN_FROM_SUPPORT==")

sequence_server = SequenceServerApi(base_url, api_token=api_token)

# Get instance configuration
print(sequence_server.get_configuration())

# Get databases with the basic set of attributes
print(sequence_server.get_databases())

# Get databases with a full set of attributes
print(sequence_server.get_databases(full_response=True))

# Select databases to query e.g. here we're selecting all nucleotide databases
databases = [db["id"] for db in sequence_server.get_databases() if db["type"] == "nucleotide"]

blast_search_type = "tblastn"
query_seq = "QRPSEEKDRKERRRAQRCAGRRAAYRKGCEKAGKLRRKGVARASREGLKISDATAALDLR\nAQTQAQPDFGQLDHQQPQHHHQQQQPPQQQQQQPPPPQQQQQPQHPQQQHNQNPESRPHH\nHLPQQHHHQHHPGNHLHSGDSGGGIGGGGGGGGGGGGGGGGGGGGGGGGGSAGGVAVVAG"

advanced_opts = "-evalue 1.0e-8"

# Submit a BLAST job and get its ID back
job_id = sequence_server.submit_blast_job(blast_search_type, query_seq, databases, advanced_opts)

# Poll for a response, jobs can take a while depending on the DB size and query complexity
response = sequence_server.poll_job(job_id)

# Get the results of the job in selected format
# Available formats: "xml", "std_tsv", "full_tsv"
print(sequence_server.get_job_result(job_id, "xml"))

Command-line API for SequenceServer

This document describes how to access SequenceServer functionality programmatically using the command line. The concept can be extended to R or any other language that can make HTTP requests.

The documentation is based on version 2.0.0.rc4

Example invocations use curl and jq.

$BASEURL in the examples is the URL of your SequenceServer instance. E.g. http://localhost:4567 if you are running on default localhost URL.

The accompanying script blastnAllDbs.sh is a working shell script to submit a BLAST job and get results.

Getting list of databases

GET: /searchdata.json

In order to submit a Blast job, you have to know the IDs of the Blast databases. This endpoint retrieves information about the databases in JSON format.

curl $BASEURL/searchdata.json | jq --raw-output '.database[].id'

The above command gets the IDs of the databases

Submitting a query

POST: /

Form parameters

• method. The name of the blast search to use (blastn, blastp, tblastn etc)
• sequence The query sequence
• databases[] One or more Ids of Blast databases to search
• advanced Additional options, e.g evalue, gapopen, gapextend etc

Responses

Successful submission results in a 303 HTTP status code.

• Code 303
• Location header is a link to the submitted job ID

Examples

1. To query a single database using blastn:

   curl -v -X POST -Fsequence=ATGTTACCACCAACTATTAGAATTTCAG -Fmethod=blastn -Fdatabases[]=3c0a5bc06f2596698f62c7ce87aeb62a $BASEURL

2. To query multiple databases, add extra -Fdatabases[] arguments, e.g.

   curl -v -X POST -Fsequence=ATGTTACCACCAACTATTAGAATTTCAG -Fmethod=blastn -Fdatabases[]=3c0a5bc06f2596698f62c7ce87aeb62a -Fdatabases[]=2f8c0e19d8d5b8ab225962d7284a6cbf $BASEURL

3. Getting location header - you need this in order to retrieve the results

   jobUrl=$(curl -v -X POST -Fsequence=ATGTTACCACCAACTATTAGAATTTCAG -Fmethod=blastn -Fdatabases[]=3c0a5bc06f2596698f62c7ce87aeb62a --write-out '%{redirect_url}' $BASEURL)

4. Altering the evalue threshold and adding a gap penalty:

   curl -v -X POST -Fsequence=ATGTTACCACCAACTATTAGAATTTCAG -Fmethod=blastn -Fdatabases[]=3c0a5bc06f2596698f62c7ce87aeb62a -Fadvanced="-evalue 1.0e-8 -gapopen 1 -gapextend 1" $BASEURL

Retrieving results

GET: /{jobId}.json

Path variables

• jobId The Job Id

Responses

• Code: 202 The Blast job is still running
• Code: 200 The job is complete, results are in JSON format

Examples

curl -o myresults.json $BASEURL/069b56c8-25bd-451e-b117-dc996a1aed24.json

Results in other formats

GET: /download/{jobId}.{format}

Path variables

• jobId the Job ID retrieved after submission
• format is one of xml, std_tsv or full_tsv

Examples

curl -o myresults.xml $BASEURL/download/069b56c8-25bd-451e-b117-dc996a1aed24.xml
curl -o myresults.tsv $BASEURL/download/069b56c8-25bd-451e-b117-dc996a1aed24.std_tsv
curl -o myresults-full.tsv $BASEURL/download/069b56c8-25bd-451e-b117-dc996a1aed24.full_tsv

Downloading hits

Download hits in FASTA format.

POST: /get_sequence

Form parameters

• sequence_ids A comma-separated list of sequence IDs
• database_ids A comma-separated list of database Ids

Examples

curl -X POST -Fsequence_ids=SPAC1002.01,SPAC1002.02 -Fdatabase_ids=2f8c0e19d8d5b8ab225962d7284a6cbf  $BASEURL/get_sequence

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