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

genome-analysis java-8 regulation

Last synced: 16 days ago
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Java Clients for the Regulatory Sequence Analysis Tools (RSAT) REST API

• Host: GitHub
• URL: https://github.com/bblodfon/rsat-rest-java-clients
• Owner: bblodfon
• Created: 2019-04-26T08:53:36.000Z (over 5 years ago)
• Default Branch: master
• Last Pushed: 2019-04-26T08:54:58.000Z (over 5 years ago)
• Last Synced: 2024-10-24T03:51:25.609Z (about 2 months ago)
• Topics: genome-analysis, java-8, regulation
• Language: Java
• Size: 22.5 KB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
# rsat-rest-java-clients

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

[RESTful API](http://rsat-tagc.univ-mrs.fr/rest/). 

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

```