The jpredapir
package provides functions to submit, check status, and
retrieve results from JPred: A Secondary Structure Prediction Server
(JPred).
jpredapir
librarylibrary(jpredapir)
jpredapir
package help messagelibrary(jpredapir) help("jpredapir")
jpredapir
package versionpackageVersion("jpredapir")
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.
raw
sequencesubmit(mode = "single", user_format = "raw", seq = "MQVWPIEGIKKFETLSYLPP")
raw
format using file
parametersubmit(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")
fasta
format using file
parametersubmit(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")
fasta
format using file
parametersubmit(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")
fasta
formatsubmit(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")
msf
formatsubmit(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")
blc
formatsubmit(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")
jobid
status(jobid = "jp_K46D05A")
jobid
and retrieve resultsstatus(jobid = "jp_K46D05A", results_dir_path = "jpred_sspred/results")
jobid
, retrieve results, and decompress archivestatus(jobid = "jp_K46D05A", results_dir_path = "jpred_sspred/results", extract = TRUE)
jobid
get_results(jobid = "jp_K46D05A", results_dir_path = "jpred_sspred/results")
jobid
and decompress archiveget_results(jobid = "jp_K46D05A", results_dir_path = "jpred_sspred/results", extract = TRUE)
quota(email = "name@domain.com")
check_rest_version()
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