Submit job to JPred REST interface.

Source: R/api.R

Submit job to JPred REST API.

submit(mode, user_format, file = NULL, seq = NULL, skipPDB = TRUE,
  email = NULL, name = NULL, silent = FALSE,
  host = "http://www.compbio.dundee.ac.uk/jpred4/cgi-bin/rest",
  suffix = "job")

Arguments

mode

Submission mode, possible values: "single", "batch", "msa".
user_format

Submission format, possible values: "raw", "fasta", "msf", "blc".
file

File path to a file with the job input (sequence or msa).
seq

Alternatively, amino acid sequence passed as string of single-letter code without spaces, e.g. --seq=ATWFGTHY
skipPDB

Should the PDB query be skipped? (default = TRUE)
email

For a batch job submission, where to send the results?
name

A name for the job.
silent

Should the work be done silently? (default = FALSE)
host

JPred host address.
suffix

Host address suffix.

Value

Response.

Examples

# NOT RUN {
## Not run ---
example_path <- system.file("exampledata", package = "jpredapir")
submit(mode = "single", user_format = "raw", seq = "MQVWPIEGIKKFETLSYLPP")
submit(mode = "single", user_format = "raw",
       file = file.path(example_path, "single_raw.example"))
submit(mode = "single", user_format = "fasta",
       file = file.path(example_path, "single_fasta.example"))
submit(mode = "batch", user_format = "fasta",
       file = file.path(example_path, "batch_fasta.example"), email = "name@domain.com")
submit(mode = "msa", user_format = "fasta",
       file = file.path(example_path, "msa_fasta.example"), email = "name@domain.com")
submit(mode = "msa", user_format = "msf",
       file = file.path(example_path, "msa_msf.example"), email = "name@domain.com")
submit(mode = "msa", user_format = "blc",
       file = file.path(example_path, "msa_blc.example"), email = "name@domain.com")
# }