Documentation

Use the RESTful API to programmatically submit, retrieve, and delete jobs from LIST-S2. This can be done through calls to the endpoints or by using our Python API wrapper.

You can download the Python API wrapper here: api.py

Requires: Python 3, requests

Note: Jobs will be stored for at least 14 days, afterwards they may be deleted without notice.

Python API Wrapper Manual

API

usage: api.py [-h] {submit,get,delete} ...

Functional API for LIST-S2 RESTful web service

optional arguments:
-h, --help           show this help message and exit

Commands:
{submit,get,delete}  Choose an action to take
submit             Submit job(s)
get                Get job(s)
delete             Delete job(s)

API SUBMIT

usage: api.py submit [-h] [-e EMAIL] (-f FILE | -d DIRECTORY)

Outputs a file <batch_id>.batch.txt containing job information. Use this file
to retrieve job status/results by running 'api.py get -f <batch_id>.batch.txt'

optional arguments:
  -h, --help            show this help message and exit
  -e EMAIL, --email EMAIL
                        Send updates to this email when job is
                        submitted/started/completed (will not be saved)

required arguments:
  Choose one method to select FASTA sequences to submit

  -f FILE, --file FILE  FASTA file(s) with labelled sequences
  -d DIRECTORY, --directory DIRECTORY
                        Directory containing FASTA files with labelled
                        sequences

API GET

usage: api.py get [-h] [-o [OUTFILE]] [-s] (-f FILE | -j JOB | -b BATCH)

optional arguments:
  -h, --help            show this help message and exit
  -o [OUTFILE], --outfile [OUTFILE]
                        Write results to outfile instead of stdout, defaults
                        to stdout
  -s, --slim            Retrieve a slim version of the job(s) without results
  -t {tab,json}, --type {tab,json}
                        Data type to return, either tabular or json. Default:
                        tab

required arguments:
  Choose one method to select jobs/batches to retrieve status/results

  -f FILE, --file FILE  Retrieve status/results for job submission batch file
  -j JOB, --job JOB     Job ID to retrieve
  -b BATCH, --batch BATCH
                        Batch ID to retrieve

API DELETE

usage: api.py delete [-h] (-f FILE | -j JOB | -b BATCH)

optional arguments:
  -h, --help            show this help message and exit

required arguments:
  Choose one method to select jobs/batches to delete

  -f FILE, --file FILE  Job submission batch file for which to delete jobs
  -j JOB, --job JOB     Job ID to delete
  -b BATCH, --batch BATCH
                        Batch ID to delete

Deleteriousness

There is no ideal way to decide on a cut-off for a binary deleterious/benign decision. Since predictors are not perfect, i.e AUC is less than 1, any cut-off value is likely to leave deleterious residues identified as benign and to wrongly identify benign residues as deleterious. Therefore, we recommend that each researcher determine a cut off-value that is best suited to their tolerance of false positives/negatives. However, some users may prefer to use a generic cut-off, in this case we suggest the LIST-S2 score of 0.85 to be used as a cut-off such that mutations with a scores of 0.85 or higher to be considered as deleterious and those with a score less than 0.85 as benign.

Job Deletion Policy

Jobs will be stored for at least 14 days, afterwards they may be deleted without notice.

Versions

LIST-S2: v1.10 (2020)