Web Scraping in R with encode method
Hello, I need to do a web-scraping of the webpage below. I need to submit the form with some specific values. After submitting the form, I need to import the data into the R (table of the link "View results as text file") in a data.frame. I tried to make the submission using the following code, but I did not get good results:
library(rvest)
library(httr)
POST(
url = "http://tempest.wellesley.edu/~btjaden/TargetRNA2/advanced.html",
encode = "form",
body=list(
`text` = "Pediococcus pentosaceus SL4",
`sequence` = ">RyhB GCGATCAGGAAGACCCTCGCGGAGAACCTGAAAGCACGACATTGCTCACATTGCTTCCAGTATTACTTAGCCAGCCGGGTGCTGGCTTTT",
`sRNA_subregions` = "on",
`window` = "10",
`before` = "10",
`after` = "20",
`seed` = "7",
`interaction_region` = "20",
`candidate_targets` = "",
`mRNA_accessibility` = "",
`sigle_target` = "",
`pvalue`= "0.05",
`max_interactions`="400"
),
verbose()
) -> res
content(res, as="parsed")
Can someone help me? I would greatly appreciate it. Thanks
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Jean-Karim Heriche
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tatty_dk •
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tatty_dk •
1 answer
Check the docs of the rvest package. There's a submit_form() function that you can use with a set_values() function. Try something like:
url <- "http://tempest.wellesley.edu/~btjaden/TargetRNA2/advanced.html"
page <- html_session(url)
form <- html_form(page)
form <- set_values(form, ...)
submit_form(page, form)
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Jean-Karim Heriche
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This looks like plain programming to me, rather than specific bioinformatics. As such it's more suitable for stackoverflow.
In addition to not being a bioinformatics question, the question is poorly formulated. What is the desired outcome ? What is the outcome produced by the code and why is it "not good" ?