The maxium mutation number returned per request is 10,000. Any result larger than this number will get a link to get the result for next page.
All request should from USC inner IP address.
API sends a response as a JSON object.
{
"status": "success/fail"
"data": [ ... ],
"format": "...",
"header":[...],
"next_page":""
}
The following table lists all API endpoints currently available at
/api
| API endpoint | Description |
|---|---|
/ |
Retrieve meta-information about dataset. |
/header/<string:dataset name> |
Get all headers name and id for a dataset |
/anno_tree/<string:dataset name> |
Get structured headers name and id for a dataset |
/origin/<string:dataset name> |
Retrieve links for download origin files. |
/variant/<string:dataset name> |
Get single variant by chromosomal position or identifier. |
/region/<string:dataset name> |
Get all variants within a chromosomal region. |
/gotopage/<string:query id>/<int:page number> |
Get the data for a certain query of certain page number. |
/gene |
Get the genome interval for a gene. |
/batch/<string:dataset name> |
Get all variants in a region. Store the result in a temporary file and return the link for that file. |
To get annotation headers, send GET request to
/header/<string:dataset name>
e.g. /header/HRC
Return example:
{
4:"ANNOVAR_ensembl_Effect",
5:"ANNOVAR_ensembl_Transcript_ID",
...
}
To get structured annotation headers, send GET request to
/anno_tree/<string:dataset name>
e.g. /anno_tree/HRC
Return example:
{"header_tree_array":[
{"detail":"",
"id":375,
"name":"1000Gp3",
"parent_id":0},
...
]
}
To download all original data files, request the download url by
/api/origin/<string:dataset name>
Return example:
{
4:"ANNOVAR_ensembl_Effect",
5:"ANNOVAR_ensembl_Transcript_ID",
...
}
####3.3.1
To query all variants within a region, send GET request to
/region/<string:dataset name>.
The following table lists all supported parameters.
| Parameter | Required | Description |
|---|---|---|
chrom |
Yes | Chromosome name. |
start |
Yes | Chromosomal start position in base-pairs. |
end |
Yes | Chromosomal end position in base-pairs. |
headers |
Optional | Header ids, seperated by %20 |
| Examples: |
/region/HRC?chrom=18&start=10&end=50000&headers=1%202%203%204%205
{
"data": [
[
"18",
"10636",
"A",
"C",
"upstream|upstream|downstream|downstream",
"ENST00000572573|ENST00000575820|ENST00000572062|ENST00000572608"
],
[
"18",
"10644",
"C",
"G",
"upstream|upstream|downstream|downstream",
"ENST00000572573|ENST00000575820|ENST00000572062|ENST00000572608"
],
...
],
"format": "json",
"headers": {
"0": "chr",
"1": "pos",
"2": "ref",
"3": "alt",
"4": "ANNOVAR_ensembl_Effect",
"5": "ANNOVAR_ensembl_Transcript_ID"
},
"next_page": "http://bioghost.usc.edu:5000/nextpage/ca2c39d1-6dfd-4c11-8292-478298a7e9ed",
"page_id": "ca2c39d1-6dfd-4c11-8292-478298a7e9ed",
"page_info": {
"page_num": 1,
"page_size": 100,
"total_page": 3
}
}
####3.3.2
To get certain page of a query, retrieve it by page_id. Send GET request to
/gotopgae/<string:page id>/<int:page number>
Examples:
/gotopage/ca2c39d1-6dfd-4c11-8292-478298a7e9ed/2
Response
Same as 3.1.1
To query a single variant, send GET request to
http://bioghost.usc.edu:5000/api/variant.The following table lists all supported parameters.
| Parameter | Required | Description |
|---|---|---|
chrom |
Yes | Chromosome name. |
pos |
Yes | Chromosomal position in base-pairs. |
ref |
Optional | Reference alle. |
alt |
Optional | Alternative alle |
Examples:
http://bioghost.usc.edu:5000/api/variant?chrom=chr2&pos=100008&ref=T&alt=A
http://bioghost.usc.edu:5000/api/variant?chrom=chr2&pos=100008
to do
To query a batch of variants, send GET request to
http://bioghost.usc.edu:5000/api/batch/<string:dataset name>
Parameters are the same with region query.
todo