NAME

Package software_handler - Handler for pipeline software


SYNOPSIS

Contains all functions to deal with extern pipeline softwares

Provided functions :


EXPORT

Exported functions :


FUNCTIONS

execute_blast

The function will execute the alignment step with Blast on the reference against all other files.

execute_carnac

The function will carnac on conserved regions found by the previous step.

execute_masking

The function will execute the masking step on the reference file and the other genomes if there's a genbank annotation file aside.

execute_rnaz

The function will RNAz on conserved regions found by the previous step.

execute_structure

The function will execute carnac and/or RNAz on conserved regions found by the previous step.

execute_yass

The function will execute the alignment step with Yass on the reference against all other files.

find_conserved_regions

The function will execute the finding conserved regions step according to alignments (Yass and/or Blast).

get_results_rnaz

The function will execute and deal with RNA predicted files from RNAz.


AUTHOR

Benjamin Grenier-Boley <benjamin.grenier-boley@inria.fr>