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