I have been trying to access an online API for bioinformatic purposes. The API was listed in their website with examples using curl. The examples they used is:
$ curl --data "method=smm&sequence_text=SLYNTVATLYCVHQRIDV&allele=HLA-A*01:01&length=9" http://tools-cluster-interface.iedb.org/tools_api/mhci/
Using an online unix terminal, I can get the correct output: Unix curl output
I tried to setup an R script using httr:
library(httr)
url="http://tools-cluster-interface.iedb.org/tools_api/mhci/"
results=POST(url,body="method=smm&sequence_text=SLYNTVATLYCVHQRIDV&allele=HLA-A*01:01&length=9")
content(results,"text")
However, the results I got do not contain useful information
[1] "Available methods:\nann\ncomblib_sidney2008\nconsensus\nnetmhccons\nnetmhcpan\nnetmhcstabpan\npickpocket\nrecommended\nsmm\nsmmpmbec\n\n* Please go to the link below for usage info:\nhttp://tools.iedb.org/main/html/tools_api.html\n"
I just want to know 1) if my script is the correct way to reflect their API method with curl? 2) how to use their api in R?
I used curlconverter to process the curl command line:
library(curlconverter)
library(httr)
curl_line <- 'curl --data "method=smm&sequence_text=SLYNTVATLYCVHQRIDV&allele=HLA-A*01:01&length=9" http://tools-cluster-interface.iedb.org/tools_api/mhci/'
straighten(curl_line) %>%
make_req() -> req
req[[1]]
## function ()
## httr::VERB(verb = "POST", url = "http://tools-cluster-interface.iedb.org/tools_api/mhci/",
## body = list(method = "smm", sequence_text = "SLYNTVATLYCVHQRIDV",
## allele = "HLA-A*01:01", length = "9"))
## <environment: 0x7fb1ba2b2d40>
Which can be used directly:
content(req[[1]]())
## [1] "allele\tseq_num\tstart\tend\tlength\tpeptide\tic50\tpercentile\trank\nHLA-A*01:01\t1\t2\t10\t9\tLYNTVATLY\t1286.92\t1.3\nHLA-A*01:01\t1\t4\t12\t9\tNTVATLYCV\t6061.08\t5.5\nHLA-A*01:01\t1\t3\t11\t9\tYNTVATLYC\t27896.52\t21\nHLA-A*01:01\t1\t8\t16\t9\tTLYCVHQRI\t36774.77\t24\nHLA-A*01:01\t1\t5\t13\t9\tTVATLYCVH\t49607.80\t30\nHLA-A*01:01\t1\t10\t18\t9\tYCVHQRIDV\t56565.29\t32\nHLA-A*01:01\t1\t7\t15\t9\tATLYCVHQR\t83090.24\t39\nHLA-A*01:01\t1\t1\t9\t9\tSLYNTVATL\t85418.12\t40\nHLA-A*01:01\t1\t6\t14\t9\tVATLYCVHQ\t282195.45\t68\nHLA-A*01:01\t1\t9\t17\t9\tLYCVHQRID\t491529.97\t79\n"
but can be converted to:
POST(url = "http://tools-cluster-interface.iedb.org/tools_api/mhci/",
body = list(method = "smm",
sequence_text = "SLYNTVATLYCVHQRIDV",
allele = "HLA-A*01:01",
length = "9")) %>%
content()
## [1] "allele\tseq_num\tstart\tend\tlength\tpeptide\tic50\tpercentile\trank\nHLA-A*01:01\t1\t2\t10\t9\tLYNTVATLY\t1286.92\t1.3\nHLA-A*01:01\t1\t4\t12\t9\tNTVATLYCV\t6061.08\t5.5\nHLA-A*01:01\t1\t3\t11\t9\tYNTVATLYC\t27896.52\t21\nHLA-A*01:01\t1\t8\t16\t9\tTLYCVHQRI\t36774.77\t24\nHLA-A*01:01\t1\t5\t13\t9\tTVATLYCVH\t49607.80\t30\nHLA-A*01:01\t1\t10\t18\t9\tYCVHQRIDV\t56565.29\t32\nHLA-A*01:01\t1\t7\t15\t9\tATLYCVHQR\t83090.24\t39\nHLA-A*01:01\t1\t1\t9\t9\tSLYNTVATL\t85418.12\t40\nHLA-A*01:01\t1\t6\t14\t9\tVATLYCVHQ\t282195.45\t68\nHLA-A*01:01\t1\t9\t17\t9\tLYCVHQRID\t491529.97\t79\n"
And, you can get your data frame with:
library(readr)
library(httr)
library(magrittr)
POST(url = "http://tools-cluster-interface.iedb.org/tools_api/mhci/",
body = list(method = "smm",
sequence_text = "SLYNTVATLYCVHQRIDV",
allele = "HLA-A*01:01",
length = "9")) -> res
content(res, as="text") %>%
read_delim(delim="\t")
## # A tibble: 10 × 9
## allele seq_num start end length peptide ic50 percentile
## <chr> <int> <int> <int> <int> <chr> <dbl> <dbl>
## 1 HLA-A*01:01 1 2 10 9 LYNTVATLY 1286.92 1.3
## 2 HLA-A*01:01 1 4 12 9 NTVATLYCV 6061.08 5.5
## 3 HLA-A*01:01 1 3 11 9 YNTVATLYC 27896.52 21.0
## 4 HLA-A*01:01 1 8 16 9 TLYCVHQRI 36774.77 24.0
## 5 HLA-A*01:01 1 5 13 9 TVATLYCVH 49607.80 30.0
## 6 HLA-A*01:01 1 10 18 9 YCVHQRIDV 56565.29 32.0
## 7 HLA-A*01:01 1 7 15 9 ATLYCVHQR 83090.24 39.0
## 8 HLA-A*01:01 1 1 9 9 SLYNTVATL 85418.12 40.0
## 9 HLA-A*01:01 1 6 14 9 VATLYCVHQ 282195.45 68.0
## 10 HLA-A*01:01 1 9 17 9 LYCVHQRID 491529.97 79.0
## # ... with 1 more variables: rank <chr>