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GETTING_STARTED.md

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Webstr API Getting Started GUIDE

How to access the WebSTR-API?

WebSTR-API provides access to the data via different “endpoints” - addresses on the url that are formed in a certain way. To access endpoints you can either use the curl tool in the Terminal or simply edit these the following links directly in your Browser. It is also possible to use WebSTR-API in your code, see Python and R examples at the bottom of this page.

WebSTR-API output

Default output is in JSON format, details for each endpoint are described in the documentation - http://webstr-api.ucsd.edu/docs It is also possible to download results in a csv format by adding "&download=True" to each request. For example: https://webstr-api.ucsd.edu/repeats?gene_names=HTT&download=True will download a csv will all repeats associated with the HTT gene in repeats.scv file.

Most common queries to WebSTR-API

Getting repeats

If you are interested in extracting STRs located in the genomic region of your interest, “repeats” endpoint would be the most important. It is possible to access genomic region of interest via genomic coordinates, common gene names or Ensemble IDs.

Access repeats via genomic coordinates:

Example request for chromosome 4, coordinates 3186810-4121716:

http://webstr-api.ucsd.edu/repeats?region_query=4:3186810-4121716

Example output:

[{"repeat_id":86397,"chr":"chr4","start":3186839,"end":3186860,"msa":"T,T,T,T,T,T,T,T,T,T,T,T,T,T,T,T,T,T,T,T,T,T",
"motif":"T","period":1,"copies":22,"ensembl_id":"ENSG00000197386","strand":"+","gene_name":"HTT",
"gene_desc":"huntingtin","total_calls":29,"frac_variable":0.896551724137931,"avg_size_diff":3.68965517241379},
{"repeat_id":1550762,"chr":"chr4","start":3313970,"end":3313989,"msa":null,"motif":"AAAT",
"period":4,"copies":5,"ensembl_id":"ENSG00000248840","strand":"+","gene_name":null,"gene_desc":null,
"total_calls":null,"frac_variable":null,"avg_size_diff":null},
....
]

Access repeats via common gene names: http://webstr-api.ucsd.edu/repeats?gene_names=HTT

Access repeats via EnsembleID: http://webstr-api.ucsd.edu/repeats?ensembl_ids=ENSG00000197386

To get repeats from several genes, chain gene_names parameters together in the following manner: https://webstr-api.ucsd.edu/repeats/?gene_names=HTT&gene_names=AGRN

Getting extended information for a repeat of interest

You will need a repeat id number from our database, available via repeats endpoint, see example above. Example request: http://webstr-api.ucsd.edu/repeatinfo/?repeat_id=1

Getting extended information for a gene of interest:

Via gene name get gene features: http://webstr-api.ucsd.edu/genefeatures/?gene_names=HTT

Using the API from Python

Here is an example of importing repeats for genes of interest into a pandas DataFrame directly from the API using requests library.

import requests 
import pandas as pd

resp = requests.get('http://webstr-api.ucsd.edu/repeats/?gene_names=HTT&gene_names=AGRN'
df_repeats = pd.DataFrame.from_records(resp.json())

Using the API from R

The same in R can be achieved using httr and jsonlite packages.

library(httr)
library(jsonlite)

res = GET("http://webstr-api.ucsd.edu/repeats/?gene_names=HTT&gene_names=AGRN")
repeats = fromJSON(rawToChar(res$content))