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https://github.com/bblodfon/rsat-rest-java-clients

Java Clients for the Regulatory Sequence Analysis Tools (RSAT) REST API

https://github.com/bblodfon/rsat-rest-java-clients

Science Score: 13.0%

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Keywords

genome-analysis java-8 regulation
Last synced: 5 months ago · JSON representation

Repository

Java Clients for the Regulatory Sequence Analysis Tools (RSAT) REST API

Basic Info
  • Host: GitHub
  • Owner: bblodfon
  • Language: Java
  • Default Branch: master
  • Size: 22.5 KB
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
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Topics
genome-analysis java-8 regulation
Created almost 7 years ago · Last pushed almost 7 years ago
Metadata Files
Readme

README.md

rsat-rest-java-clients

This module is a Java Client for the Regulatory Sequence Analysis Tools (RSAT) RESTful API.

Currently, only one tool is supported with a Java Client, namely the fetch-sequences tool. This tool is used to retrieve genome sequences for a set of coordinates specified in a bed file (either from a resource URL through the GET and POST methods or from a local .bed file through POST).

Install

Tested with maven version 3.6.0, compiled with Java 8 mvn clean install

Examples

  • When using no arguments, you get the list of available parameters: ``` java -cp target/java.clients-1.0-jar-with-dependencies.jar clients.FetchSequencesClient

Options preceded by an asterisk are required. Usage: clients.FetchSequencesClient [options] Options: * --requestMethod, -m The HTTP request method: GET or POST --responseContentType, -c The response content type: json or text Default: json --genome, -g Genome version (e.g. mm9, hg19) Default: mm9 --header, -h Format for sequence headers: UCSC or galaxy Default: galaxy --resourceURL, -u URL file resource --resourceBedFile, -f File in .bed format ```

  • Using the GET HTTP method to retrieve the sequences from a URL resource: java -cp target/java.clients-1.0-jar-with-dependencies.jar clients.FetchSequencesClient -m=GET -c=json -u=http://rsat-tagc.univ-mrs.fr/rsat/demo_files/fetch-sequences_Schmidt_2011_mm9_CEBPA_SWEMBL_R0.12_702peaks.bed -g=mm9 -h=galaxy

  • Using the POST HTTP method to retrieve the sequences from a URL resource: java -cp target/java.clients-1.0-jar-with-dependencies.jar clients.FetchSequencesClient -m=POST -c=text -u=http://rsat-tagc.univ-mrs.fr/rsat/demo_files/fetch-sequences_Schmidt_2011_mm9_CEBPA_SWEMBL_R0.12_702peaks.bed -g=mm9 -h=galaxy

  • Using the POST HTTP method to retrieve the sequences from a local .bed file resource: java -cp target/java.clients-1.0-jar-with-dependencies.jar clients.FetchSequencesClient -m=POST -c=json -f=src/main/resources/test.bed -g=mm9 -h=galaxy

Owner

  • Name: John Zobolas
  • Login: bblodfon
  • Kind: user

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