The jpredapir package provides functions to submit, check status, and retrieve results from JPred: A Secondary Structure Prediction Server (JPred).

Importing jpredapir library

library(jpredapir)

Print jpredapir package help message

library(jpredapir)
help("jpredapir")

Print jpredapir package version

packageVersion("jpredapir")

Submitting jobs to JPred server

Note that the examples below are not run, due to needing access to the server. They do illustrate how to submit jobs in various formats, however.

There are various example inputs in the exampledata directory that accompanies this package. The full list of files can be found by running the command below on your own installation:

dir(system.file("exampledata", package = "jpredapir"), full.names = TRUE)

These files demonstrate the different types of input that can be used with jpred, and also provide examples that can be used yourself for testing submission and the returned results.

Submit a single raw sequence

submit(mode = "single", user_format = "raw", seq = "MQVWPIEGIKKFETLSYLPP")

Submit single sequence in raw format using file parameter

submit(mode = "single", user_format = "raw", file = system.file("exampledata/single_raw.example", package = "jpredapir"))

Content of single_raw.example file:

cat(scan(system.file("exampledata/single_raw.example", package = "jpredapir"), what = character(), sep = "\n", quiet = TRUE), sep = "\n")

Submit single sequence in fasta format using file parameter

submit(mode = "single", user_format = "fasta", file = system.file("exampledata/single_fasta.example", package = "jpredapir"))

Content of single_fasta.example file:

cat(scan(system.file("exampledata/single_fasta.example", package = "jpredapir"), what = character(), sep = "\n", quiet = TRUE), sep = "\n")

Submit multiple sequences in fasta format using file parameter

submit(mode = "batch", user_format = "fasta", file = system.file("exampledata/batch_fasta.example", package = "jpredapir"), email = "name@domain.com")

Content of batch_fasta.example file:

cat(scan(system.file("exampledata/batch_fasta.example", package = "jpredapir"),
  what = character(), sep = "\n", quiet = TRUE), sep = "\n")

Submit multiple sequence alignment files in fasta format

submit(mode = "msa", user_format = "fasta", file = system.file("exampledata/msa_fasta.example", package = "jpredapir"), email = "name@domain.com")

Content of msa_fasta.example file:

cat(scan(system.file("exampledata/msa_fasta_short.example", package = "jpredapir"), what = character(),
sep = "\n", quiet = TRUE), sep = "\n")

Submit multiple sequence alignment files in msf format

submit(mode = "msa", user_format = "msf", file = system.file("exampledata/msa_msf.example", package = "jpredapir"), email = "name@domain.com")

Content of msa_msf.example file:

cat(scan(system.file("exampledata/msa_msf.example", package = "jpredapir"), what = character(),
sep = "\n", quiet = TRUE), sep = "\n")

Submit multiple sequence alignment files in blc format

submit(mode = "msa", user_format = "blc", file = system.file("exampledata/msa_blc.example", package = "jpredapir"), email = "name@domain.com")

Content of msa_blc.example file:

cat(scan(system.file("exampledata/msa_blc_short.example", package = "jpredapir"), what = character(),
sep = "\n", quiet = TRUE), sep = "\n")

Check job status on JPred server

Check single job status using jobid

status(jobid = "jp_K46D05A")

Check single job status using jobid and retrieve results

status(jobid = "jp_K46D05A", results_dir_path = "jpred_sspred/results")

Check single job status using jobid, retrieve results, and decompress archive

status(jobid = "jp_K46D05A", results_dir_path = "jpred_sspred/results", extract = TRUE)

Retrieve results from JPred server

Retrieve results using jobid

get_results(jobid = "jp_K46D05A", results_dir_path = "jpred_sspred/results")

Retrieve results using jobid and decompress archive

get_results(jobid = "jp_K46D05A", results_dir_path = "jpred_sspred/results", extract = TRUE)

Check quota

Check how many jobs you have already submitted on a given day

quota(email = "name@domain.com")

Check JPred REST interface version

Check version of JPred REST interface

check_rest_version()


MoseleyBioinformaticsLab/jpredapir documentation built on May 20, 2019, 1:13 p.m.