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).
Tested with maven version 3.6.0, compiled with Java 8
mvn clean install
- 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
GETHTTP 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:https://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
POSTHTTP 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:https://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
POSTHTTP 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