Command line tools

The source code repository builds a command line tool feature-tools that creates new features from an input file in tab-delimited plain text format.

The tools/target directory contains the command line tools in various compression format.

-rw-r--r--   1 pbashyal  827464065  31645595 Jan  5 16:08 feature-tools-1.0-SNAPSHOT-bin.tar.bz2
-rw-r--r--   1 pbashyal  827464065  31608784 Jan  5 16:08 feature-tools-1.0-SNAPSHOT-bin.tar.gz
-rw-r--r--   1 pbashyal  827464065  31609718 Jan  5 16:08 feature-tools-1.0-SNAPSHOT-bin.zip

The artifacts contain the following directory structure.

feature-tools-1.0-SNAPSHOT
├── COPYING
├── COPYING.LESSER
├── bin
│   ├── feature-tools
│   └── feature-tools.bat
└── lib
    ├── annotations-2.0.1.jar
    ├── aopalliance-1.0.jar

bin/feature-tools is the command line tool to interact with the feature service.

About

$ feature-tools -a
feature-tools 1.0-SNAPSHOT
Commit: 8d68ef17deeaa3c2a1394e7c8090eae5c07f393d  Build: 2015-02-26
Copyright (c) 2014-2015 National Marrow Donor Program (NMDP)
Licensed GNU Lesser General Public License (LGPL), version 3 or later

Help

$ feature-tools -h
usage:
feature-tools -u http://localhost:8080/ -i requests.txt -o features.txt

arguments:
   -a, --about  display about message [optional]
   -h, --help  display help message [optional]
   -u, --endpoint-url [class java.lang.String]  endpoint URL, default http://localhost:8080/ [optional]
   -i, --input-file [class java.io.File]  input file of tab-delimited feature requests, default stdin [optional]
   -o, --output-file [class java.io.File]  output file of tab-delimited features, default stdout [optional]

Input file format

requests.txt is 4 column tab delimited text file.

HLA-V	exon	1	ACTG
HLA-V	exon	1	GACT
HLA-V	intron	1	GGTC
HLA-V	exon	2	GATT
HLA-V	exon	1	ACTG
HLA-V	exon	1	GACT
HLA-V	intron	1	GGTC
HLA-V	exon	2	GATT

Usage

feature-tools -u http://localhost:8080/ -i requests.txt -o features.txt