The jpredapir Tutorial: Using jpredapir Command Line Interface

Andrey Smelter

2018-09-24

Source: vignettes/tutorial_as_cli.Rmd

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

Command Line Interface

jpredapir command-line interface

The JPred API allows users to submit jobs from the command-line.

Usage:
    jpredapi.R submit (--mode=<mode> --format=<format>) (--file=<filename> | --seq=<sequence>) [--email=<name@domain.com>] [--name=<name>] [--rest=<address>] [--skipPDB] [--silent]
    jpredapi.R status (--jobid=<id>) [--results=<path>] [--wait=<interval>] [--attempts=<max>] [--rest=<address>] [--jpred4=<address>] [--extract] [--silent]
    jpredapi.R get_results (--jobid=<id>) [--results=<path>] [--wait=<interval>] [--attempts=<max>] [--rest=<address>] [--jpred4=<address>] [--extract] [--silent]
    jpredapi.R quota (--email=<name@domain.com>) [--silent]
    jpredapi.R check_rest_version [--rest=<address>] [--silent]
    jpredapi.R -h | --help
    jpredapi.R -v | --version

Options:
    -h, --help                 Show this help message.
    -v, --version              Show jpredapir package version.
    --silent                   Do not print messages.
    --extract                  Extract results tar.gz archive.
    --skipPDB                  PDB check.
    --mode=<mode>              Submission mode, possible values: single, batch, msa.
    --format=<format>          Submission format, possible values: raw, fasta, msf, blc.
    --file=<filename>          Filename of a file with the job input (sequence(s)).
    --seq=<sequence>           Instead of passing input file, for single-sequence submission.
    --email=<name@domain.com>  E-mail address where job report will be sent (optional for all but batch submissions).
    --name=<name>              Job name.
    --jobid=<id>               Job id.
    --results=<path>           Path to directory where to save archive with results.
    --rest=<address>           REST address of server [default: http://www.compbio.dundee.ac.uk/jpred4/cgi-bin/rest].
    --jpred4=<address>         Address of Jpred4 server [default: http://www.compbio.dundee.ac.uk/jpred4].
    --wait=<interval>          Wait interval before retrying to check job status in seconds [default: 60].
    --attempts=<max>           Maximum number of attempts to check job status [default: 10].

Find jpredapir CLI executable

To find jpredapi.R executable start your R shell and type:

shQuote(system.file("exec", "jpredapi.R", package = "jpredapir"))

Output:

'path/to/jpredapir/exec/jpredapi.R'

Submit jobs to JPred server

Submit single sequence in raw format using --seq parameter

Rscript jpredapir/exec/jpredapi.R submit --mode=single --format=raw --seq=MQVWPIEGIKKFETLSYLPP

Submit single sequence in raw format using --file parameter

Rscript jpredapir/exec/jpredapi.R submit --mode=single --format=raw --file=inst/exampledata/single_raw.example

Content of single_raw.example file:

MQVWPIEGIKKFETLSYLPPLTVEDLLKQIEYLLRSKWVPCLEFSKVGFVYRENHRSPGYYDGRYWTMWKLPMFGCTDATQVLKELEEAKKAYPDAFVRIIGFDNVRQVQLISFIAYKPPGC

Submit single sequence in fasta format using --file parameter

Rscript jpredapir/exec/jpredapi.R submit --mode=single --format=fasta --file=inst/exampledata/single_fasta.example

Content of single_fasta.example file:

>my test sequence
MQVWPIEGIKKFETLSYLPPLTVEDLLKQIEYLLRSKWVPCLEFSKVGFVYRENHRSPGYYDGRYWTMWKLPMFGCTDATQVLKELEEAKKAYPDAFVRIIGFDNVRQVQLISFIAYKPPGC

Submit multiple sequences in fasta format using --file parameter

Rscript jpredapir/exec/jpredapi.R submit --mode=batch --format=fasta --file=inst/exampledata/batch_fasta.example --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

Rscript jpredapir/exec/jpredapi.R submit --mode=msa --format=fasta --file=inst/exampledata/msa_fasta.example --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

Rscript jpredapir/exec/jpredapi.R submit --mode=msa --format=msf --file=inst/exampledata/msa_msf.example --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

Rscript jpredapir/exec/jpredapi.R submit --mode=msa --format=blc --file=inst/exampledata/msa_blc.example --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 

Rscript jpredapir/exec/jpredapi.R status --jobid=jp_K46D05A

Check single job status using jobid and retrieve results

Rscript jpredapir/exec/jpredapi.R status --jobid=jp_K46D05A --results=jpred_sspred/results

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

Rscript jpredapir/exec/jpredapi.R status --jobid=jp_K46D05A --results=jpred_sspred/results --extract

Retrieve results from JPred server

Retrieve results using jobid 

Rscript jpredapir/exec/jpredapi.R get_results --jobid=jp_K46D05A --results=jpred_sspred/results

Retrieve results using jobid and decompress archive

Rscript jpredapir/exec/jpredapi.R get_results --jobid=jp_K46D05A --results=jpred_sspred/results --extract

Check quota

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

Rscript jpredapir/exec/jpredapi.R quota --email=name@domain.com

Check JPred REST interface version

Check version of JPred REST interface

Rscript jpredapir/exec/jpredapi.R check_rest_version