service-gfe-submission

---

This repository is now obsolete. All functionality is now available in the pyGFE Github repository.

---

RESTful API for getting GFE results from raw sequence data

Further documentation is available at service-gfe-submission.readthedocs.io.

The Gene Feature Enumeration (GFE) Submission service provides an API for converting raw sequence data to GFE. It provides both a RESTful API and a simple user interface for converting raw sequence data to GFE results. Sequences can be submitted one at a time or as a fasta file. This service uses nmdp-bioinformatics/service-feature for encoding the raw sequence data and nmdp-bioinformatics/HSA for aligning the raw sequence data. A public version of this service is available for use at gfe.b12x.org.

RESTful Calls

    
# Get GFE from sequence data - in body #
curl --header "Content-type: application/json" --request POST  \
--data '{"locus":"HLA-A","sequence":"TCCCCAGACGCCGAGGATGGCCGTCATGGCGCCCCGAACCCTCCTCCTGCTACTCTCGGGGGCCCTGGCCCTGACCCAGACCTGGGCGGGTGAGTGCGGGGTCGGGAGGGAAACCGCCTCTGCGGGGAGAAGCAAGGGGCCCTCCTGGCGGGGGCGCAGGACCGGGGGAGCCGCGCCGGGACGAGGGTCGGGCAGGTCTCAGCCACTGCTCGCCCCCAGGCTCCCACTCCATGAGGTATTTCTTCACATCCGTGTCCCGGCCCGGCCGCGGGGAGCCCCGCTTCATCGCCGTGGGCTACGTGGACGACACGCAGTTCGTGCGGTTCGACAGCGACGCCGCGAGCCAGAGGATGGAGCCGCGGGCGCCGTGGATAGAGCAGGAGGGGCCGGAGTATTGGGACCAGGAGACACGGAATGTGAAGGCCCAGTCACAGACTGACCGAGTGGACCTGGGGACCCTGCGCGGCTACTACAACCAGAGCGAGGCCGGTGAGTGACCCCGGCCGGGGGCGCAGGTCAGGACCCCTCATCCCCCACGGACGGGCCAGGTCGCCCACAGTCTCCGGGTCCGAGATCCACCCCGAAGCCGCGGGACCCCGAGACCCTTGCCCCGGGAGAGGCCCAGGCGCCTTTACCCGGTTTCATTTTCAGTTTAGGCCAAAAATCCCCCCGGGTTGGTCGGGGCTGGGCGGGGCTCGGGGGACTGGGCTGACCGCGGGGTCGGGGCCAGGTTCTCACACCATCCAGATAATGTATGGCTGCGACGTGGGGTCGGACGGGCGCTTCCTCCGCGGGTACCGGCAGGACGCCTACGACGGCAAGGATTACATCGCCCTGAACGAGGACCTGCGCTCTTGGACCGCGGCGGACATGGCGGCTCAGATCACCAAGCGCAAGTGGGAGGCGGCCCATGAGGCGGAGCAGTTGAGAGCCTACCTGGATGGCACGTGCGTGGAGTGGCTCCGCAGATACCTGGAGAACGGGAAGGAGACGCTGCAGCGCACGGGTACCAGGGGCCACGGGGCGCCTCCCTGATCGCCTGTAGATCTCCCGGGCTGGCCTCCCACAAGGAGGGGAGACAATTGGGACCAACACTAGAATATCACCCTCCCTCTGGTCCTGAGGGAGAGGAATCCTCCTGGGTTCCAGATCCTGTACCAGAGAGTGACTCTGAGGTTCCGCCCTGCTCTCTGACACAATTAAGGGATAAAATCTCTGAAGGAGTGACGGGAAGACGATCCCTCGAATACTGATGAGTGGTTCCCTTTGACACCGGCAGCAGCCTTGGGCCCGTGACTTTTCCTCTCAGGCCTTGTTCTCTGCTTCACACTCAATGTGTGTGGGGGTCTGAGTCCAGCACTTCTGAGTCCCTCAGCCTCCACTCAGGTCAGGACCAGAAGTCGCTGTTCCCTTCTCAGGGAATAGAAGATTATCCCAGGTGCCTGTGTCCAGGCTGGTGTCTGGGTTCTGTGCTCTCTTCCCCATCCCGGGTGTCCTGTCCATTCTCAAGATGGCCACATGCGTGCTGGTGGAGTGTCCCATGACAGATGCAAAATGCCTGAATTTTCTGACTCTTCCCGTCAGACCCCCCCAAGACACATATGACCCACCACCCCATCTCTGACCATGAGGCCACCCTGAGGTGCTGGGCCCTGGGCTTCTACCCTGCGGAGATCACACTGACCTGGCAGCGGGATGGGGAGGACCAGACCCAGGACACGGAGCTCGTGGAGACCAGGCCTGCAGGGGATGGAACCTTCCAGAAGTGGGCGGCTGTGGTGGTGCCTTCTGGAGAGGAGCAGAGATACACCTGCCATGTGCAGCATGAGGGTCTGCCCAAGCCCCTCACCCTGAGATGGGGTAAGGAGGGAGATGGGGGTGTCATGTCTCTTAGGGAAAGCAGGAGCCTCTCTGGAGACCTTTAGCAGGGTCAGGGCCCCTCACCTTCCCCTCTTTTCCCAGAGCTGTCTTCCCAGCCCACCATCCCCATCGTGGGCATCATTGCTGGCCTGGTTCTCCTTGGAGCTGTGATCACTGGAGCTGTGGTCGCTGCCGTGATGTGGAGGAGGAAGAGCTCAGGTGGAGAAGGGGTGAAGGGTGGGGTCTGAGATTTCTTGTCTCACTGAGGGTTCCAAGCCCCAGCTAGAAATGTGCCCTGTCTCATTACTGGGAAGCACCGTCCACAATCATGGGCCTACCCAGTCTGGGCCCCGTGTGCCAGCACTTACTCTTTTGTAAAGCACCTGTTAAAATGAAGGACAGATTTATCACCTTGATTACGGCGGTGATGGGACCTGATCCCAGCAGTCACAAGTCACAGGGGAAGGTCCCTGAGGACAGACCTCAGGAGGGCTATTGGTCCAGGACCCACACCTGCTTTCTTCATGTTTCCTGATCCCGCCCTGGGTCTGCAGTCACACATTTCTGGAAACTTCTCTGGGGTCCAAGACTAGGAGGTTCCTCTAGGACCTTAAGGCCCTGGCTCCTTTCTGGTATCTCACAGGACATTTTCTTCTCACAGATAGAAAAGGAGGGAGTTACACTCAGGCTGCAAGTAAGTATGAAGGAGGCTGATGCCTGAGGTCCTTGGGATATTGTGTTTGGGAGCCCATGGGGGAGCTCACCCACCTCACAATTCCTCCTCTAGCCACATCTTCTGTGGGATCTGACCAGGTTCTGTTTTTGTTCTACCCCAGGCAGTGACAGTGCCCAGGGCTCTGATGTGTCCCTCACAGCTTGTAAAGGTGAGAGCTTGGAGGACCTAATGTGTGTTGGGTGTTGGGCGGAACAGTGGACACAGCTGTGCTATGGGGTTTCTTTGCATTGGATGTATTGAGCATGCGATGGGCTGTTTAAGGTGTGACCCCTCACTGTGATGGATATGAATTTGTTCATGAATATTTTTTTCTATAGTGTGAGACAGCTGCCTTGTGTGGGACTGAG"}' \
http://gfe.b12x.org/gfe

# Sequence from GFE #
curl --header "Content-type: application/json" --request POST \
--data '{"locus":"HLA-A","gfe":"HLA-Aw1-1-7-20-10-32-7-1-1-1-6-1-5-3-5-1-0"}' \
http://gfe.b12x.org/sequence

# Get GFE from fasta file #
curl -F "verbose=1" -F "locus=HLA-A" \
-F "file=@GFE_Submission/public/downloads/FastaTest.fasta" \
http://gfe.b12x.org/fasta

# Get GFE from HML file #
curl -F "verbose=1" \
-F "file=@GFE_Submission/public/downloads/HmlTest.HML" \
http://gfe.b12x.org/hml

# Get HML file with GFE from HML  #
curl -F "verbose=1" -F "type=xml" \
-F "file=@GFE_Submission/public/downloads/HmlTest.HML" \
http://gfe.b12x.org/hml

# Get HML file with GFE from HML using nextflow #
# Faster than /hml but can not provide structures #
curl -F "verbose=1" \
-F "file=@GFE_Submission/public/downloads/HmlTest.HML" \
http://gfe.b12x.org/flowhml

Docker

The easiest way to get the service running locally, is to pull an image containing the service from docker hub. Running the following command will pull the latest GFE service image from docker hub. The image on docker hub is built from the Dockerfile in the docker directory in the github repository. Every new commit to the nmdp-bioinformatics/service-gfe-submission repository triggers a new build of the docker image on docker hub.

docker pull nmdpbioinformatics/service-gfe-submission
docker run -d --name service-gfe-submission -p 8080:5050 nmdpbioinformatics/service-gfe-submission

The -d flag runs the service in "detached-mode" in the background and -p specifies what ports to expose. Make sure the ports you expose are not already in use. If the docker container is successfuly executed then typing docker ps -a will show a new container labeled service-gfe-submission running.

Click here for more information on the publically available docker image.

Perl client example

#!/usr/bin/env perl
use strict;
use warnings;
use GFE_Client;

my $s_seq   = shift @ARGV;
my $s_locus = shift @ARGV;

# Does alignment of sequence and submission of aligned
# sequence to the GFE service.
my $o_client = GFE_Client->new();
my $rh_gfe   = $o_client->getGfe($s_locus,$s_seq);

# Print out GFE
print $$rh_gfe{gfe},"\n";

R client example

if (!is.installed('gfeClient')){
    library(devtools)
    install_github('nmdp-bioinformatics/service-gfe-submission/client-R')
}
library('gfeClient')

host <- 'http://gfe.b12x.org/'

# Get GFE from fasta file
fasta.file <- 'GFE_Submission/t/resources/fastatest1.fasta'
fasta.gfe  <- fasta2gfe(host,'HLA-A',fasta.file)

# Get sequence from
seq        <- gfe2seq(host,'HLA-A','HLA-Aw1-1-7-20-10-32-7-1-1-1-6-1-5-3-5-1-1')

# Get GFE from sequence
gfe        <- seq2gfe(host,'HLA-A',seq)

# return detailed logs
verbose    <- 1
gfe        <- seq2gfe(host,'HLA-A',seq,verbose)

# Return structure (ex. exon, 1 , TGCCCAAGCCCCTCACCCTGAGATGGG)
structure  <- 1
gfe        <- seq2gfe(host,'HLA-A',seq,verbose,structure)

Tools

./fasta2gfe [--fasta] [--locus] [--uri] [--verbose] [--help]
            -f/--fasta      Fasta file ** STDIN **
            -u/--uri        URI of feature service
            -l/--locus      HLA-Locus
            -v/--verbose    Flag for running in verbose
            -h/--help

fasta2gfe --fasta t/resources/fastatest1.fasta -l HLA-A > fastatest1.gfe.csv
cat t/resources/fastatest1.fasta | fasta2gfe -l HLA-A > fastatest1.gfe.csv

./seq2gfe [--seq] [--locus] [--uri] [--verbose] [--help]
            -s/--seq        Sequence  ** STDIN **
            -u/--uri        URI of feature service
            -l/--locus      HLA-Locus
            -v/--verbose    Flag for running in verbose
            -h/--help

seq2gfe --seq GACGGCAAGGATTACATCGCCCTGAACGAGGACCTGCGCT \
CTTGGACCGCGGCGGACATGGCGGCTCAGATCACCAAGCGCAAGTACCTGCGCT -l HLA-A > seqtest1.gfe.csv
cat GACGGCAAGGATTACATCGCCCTGAACGAGGACCTGCGCTCTTGGACCGC \
GGCGGACATGGCGGCTCAGATCACCAAGCGCAAGTACCTGCGCTCTTGGACCGC | seq2gfe -l HLA-A > seqtest1.gfe.csv

./hml2gfe [--input] [--hml] [--uri] [--verbose] [--help]
            -i/--input      HML file
            -u/--uri        URI of feature service
            -h/--hml        flag for returning HML
            -v/--verbose    Flag for running in verbose
            -h/--help

hml2gfe --input t/resources/hmltest1.HML > hmltest1.gfe.csv
hml2gfe --input t/resources/hmltest1.HML --hml > hmltest1.gfe.HML

Installing and Running Service Locally

perl cpanm --installdeps .   # Install perl dependencies
perl Makefile.PL             # Generate Makefile
make                         # Make menefest
make test                    # Run tests
make install                 # Install
plackup -E deployment  \     # Deploy
-s Starman --workers=10 \
-p 5050:8080 -a bin/app.pl      

Required Software

• Git
• clustalo
• hap1.2
• perl 5.18 or later
• nextflow

Related Links

• hub.docker.com/r/nmdpbioinformatics/service-gfe-submission
• service-gfe-submission.readthedocs.io
• github.com/nmdp-bioinformatics/service-feature
• github.com/nmdp-bioinformatics/HSA
• bioinformatics.bethematchclinical.org
• feature.nmdp-bioinformatics.org
• gfe.b12x.org