rdeer-service 1.4.1

Client-server to handle Reindeer in query mode.

RDEER-SERVICE

rdeer-service is a tool to facilitate the use of Reindeer as socket mode. It also summarize its outputs.

It is a companion to Transipedia, a web application to query easily and fastly Reindeer.

Installation

Recommanded (pip)

python3 -m pip install rdeer-service

Other (git)

git clone https://github.com/Bio2M/rdeer-service.git

How to use?

Prerequisite

You need some Reindeer indexes.

• each index must embeds additionnal file named fos.txt The fos.txt file must contain the list of sample (IN ORDER) and facultatively for each sample a count to normalize counts with the -n option (delimiter: tab)

Example of fof :

sample_A	1234567
sample_B	2367912
sample C	4562221

• The indexes built with the --disk-query option must have a empy file named disk-query. So queries will use the --disk-query option.

Start the server

the server must be in the same physical server than Reindeer, You can have multiple servers with Reindeer. Each of them must have the server.

rdeer-server /path/to/indexes

• rdeer-server listen on port 12800, you can change this with --port option.
• The server will only be able to handle indexes in the specified directory. If your indexes are spread over several directories, you may create symlinks in /path/to/indexes.
• You can add, remove or change the name of the indexes, rdeer-server takes the changes on the fly.
• It is recommanded to start rdeer-server as a daemon, using systemd, supervisord or whatever.

Use the client

The client could requests remote rdeer-server servers. You can enterely manage yours Reindeer indexes with subcommand:

• rdeer list -a to show all indexes with their status
• rdeer start <index-name> to start a index (the index name is the directory hosting the index files)
• rdeer stop <index-name> to stop a index
• rdeer check <index-name> to verify if index responding
• rdeer query <index-name> -q <query.fa> to request an index

show running indexes:

rdeer-client list

Show all indexes handled by rdeer-server

rdeer-client list -a

list all accessible indexes by rdeer-server, with status. Status are :

• available the index is not running
• loading the index is in a transitional mode until the running mode
• running the index is started, and can be resquested.

Start an index:

rdeer-client start my-index

Will starts the my-index Reindeer index. When status is running, the index is ready to respond to requests.

Query an index

rdeer-client query my-index -q fasta-query

Requests the specified index, the query file is required and must be in a fasta format.

Options of query subcommand (rdeer-client query --help):

• -q, --query to send a query file at the fasta format (required)
• -n, --normalize to obtain normalized counts
• -u, unitig-counts to obtain raw Reindeer output
• -s, --server to request rdeer-server on remote host
• -p, --port to request rdeer-server on a specified port (default: 12800)
• -o, --outfile output is stdout by default, you can specified a file