The jpredapir Tutorial: Using jpredapir as a Library

Andrey Smelter

2018-09-27

Source: vignettes/tutorial_as_library.Rmd

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)

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:

MQVWPIEGIKKFETLSYLPPLTVEDLLKQIEYLLRSKWVPCLEFSKVGFVYRENHRSPGYYDGRYWTMWKLPMFGCTDATQVLKELEEAKKAYPDAFVRIIGFDNVRQVQLISFIAYKPPGC

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:

>my test sequence
MQVWPIEGIKKFETLSYLPPLTVEDLLKQIEYLLRSKWVPCLEFSKVGFVYRENHRSPGYYDGRYWTMWKLPMFGCTDATQVLKELEEAKKAYPDAFVRIIGFDNVRQVQLISFIAYKPPGC

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:

>my_seq1
MKFLVLLFNILCLFPILGADELVMSPIPTTDVQPKVTFDINSEVSSGPLYLNPVEMAGVK
YLQLQRQPGVQVHKVVEGDIVIWENEEMPLYTCAIVTQNEVPYMAYVELLEDPDLIFFLK
EGDQWAPIPEDQYLARLQQLRQQIHTESFFSLNLSFQHENYKYEMVSSFQHSIKMVVFTP
KNGHICKMVYDKNIRIFKALYNEYVTSVIGFFRGLKLLLLNIFVIDDRGMIGNKYFQLLD
DKYAPISVQGYVATIPKLKDFAEPYHPIILDISDIDYVNFYLGDATYHDPGFKIVPKTPQ
CITKVVDGNEVIYESSNPSVECVYKVTYYDKKNESMLRLDLNHSPPSYTSYYAKREGVWV
TSTYIDLEEKIEELQDHRSTELDVMFMSDKDLNVVPLTNGNLEYFMVTPKPHRDIIIVFD
GSEVLWYYEGLENHLVCTWIYVTEGAPRLVHLRVKDRIPQNTDIYMVKFGEYWVRISKTQ
>my_seq2
MASVKSSSSSSSSSFISLLLLILLVIVLQSQVIECQPQQSCTASLTGLNVCAPFLVPGSP
TASTECCNAVQSINHDCMCNTMRIAAQIPAQCNLPPLSCSAN
>my_seq3
MEKKSIAGLCFLFLVLFVAQEVVVQSEAKTCENLVDTYRGPCFTTGSCDDHCKNKEHLLS
GRCRDDVRCWCTRNC

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:

>QUERY_1
MQVWPIEGIKKFETLSYLPPLTVEDLLKQIEYLLRSKWVPCLEFSKVGFVYRENHRSPGYYDGRYWTMWKLP
MFGCTDATQVLKELEEAKKAYPDAFVRIIGFDNVRQVQLISFIAYKPPGC
>UniRef90_Q40250_2
MKVWPPIGLKKYETLSYLPPLSDEALSKEIDYLIRNKWIPCLEFEEHGFVYREHHHSPGYYDGRYWTMWKLP
MFGCTDSAQVMKEVGECKKEYPNAFIRVIGFDNIRQVQCISFIVAKPPGV
>UniRef90_A7YVW5_3
MQVWPPLGKRKFETLSYLPPLPVDALLKQIDYLIRSGWIPCIEFTVEGFVYREHHHSPGYYDGRYWTMWKLP
MYGCTDSTQVLAEVEANKKEYPNSYIRIIGFDNKRQVQCVSFIVHTPPS-
>UniRef90_P04714_4
MQVWPPYGKKKYETLSYLPDLTDEQLLKEIEYLLNKGWVPCLEFTEHGFVYREYHASPRYYDGRYWTMWKLP
MFGCTDATQVLGELQEAKKAYPNAWIRIIGFDNVRQVQCISFIAYKPPG-
>UniRef90_W9RUU9_5
MQVWPPRGKLKFETLSYLPDLTDEQLLKEIDYLLRSNWIPCLEFEVKAHIYRENNRSPGYYDGRYWTMWKLP
MFGCTDATQVLAEVQETKKAYPDAHVRIIGFDNNRQVQCISFIAYKPPA-

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:

 /tmp/filelPdICy  MSF: 108  Type: N  January 01, 1776  12:00  Check: 2741 ..
 Name: 0_1a             Len:   108  Check:  4063  Weight:  1.00
 Name: 1_MA             Len:   108  Check:  4875  Weight:  1.00
 Name: 2_KE             Len:   108  Check:   449  Weight:  1.00
 Name: 3_NC             Len:   108  Check:  3354  Weight:  1.00
//
           0_1a  APAFSVSPAS GASDGQSVSV SVAAAGETYY IAQCAPVGGQ DACNPATATS
           1_MA  APGVTVTPAT GLSNGQTVTV SATTPGTVYH VGQCAVVEGV IGCDATTSTD
           2_KE  SAAVSVSPAT GLADGATVTV SASATSTSAT ALQCAILAGR GACNVAEFHD
           3_NC  APTATVTPSS GLSDGTVVKV AGAQAGTAYD VGQCAWVDGV LACNPADFSS
           0_1a  FTTDASGAAS FSFTVRKSYA GQTPSGTPVG SVDCATDACN LGAGNSGLNL
           1_MA  VTADAAGKIT AQLKVHSSFQ AVVANGTPWG TVNCKVVSCS AGLGSDSGEG
           2_KE  FSLSG.GEGT TSVVVRRSFT GYVPDGPEVG AVDCDTAPCE IVVGGNTGEY
           3_NC  VTADANGSAS TSLTVRRSFE GFLFDGTRWG TVDCTTAACQ VGLSDAAGNG
           0_1a  GHVALTFG
           1_MA  AAQAITFA
           2_KE  GNAAISFG
           3_NC  PGVAISFN

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:

>0_1a  Name
>1_MA  Name
>2_KE  Name
>3_NC  Name
* iteration 1
AASA
PPAP
AGAT
FVVA
STST
VVVV
STST
PPPP
AAAS
*

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()