Package software_handler - Handler for pipeline software
Contains all functions to deal with extern pipeline softwares
Provided functions :
execute_blast
execute_carnac
execute_masking
execute_rnaz
execute_yass
find_conserved_regions
get_results_rnaz
Exported functions :
execute_blast
execute_masking
execute_structure
execute_yass
find_conserved_regions
The function will execute the alignment step with Blast on the reference against all other files.
parameters :
$reference_file, the location of the reference file
$other_files, the reference on the hash table containing other files
$cmd_blast, the command to execute Blast
$blast_outdir, the outdir of alignment files
$quiet, the quiet mode
returns : nothing.
The function will carnac on conserved regions found by the previous step.
parameters :
$cmd_carnac, the command to execute caRNAc
$cmd_rnaplot, the command to execute RNAplot
$cg_seq_outdir, the outdir of conserved region
$yass_available, yass software wanted or not
$blast_available, blast software wanted or not
$yass_outdir_name, name of the outdir of yass
$blast_outdir_name, name of the outdir of Blast
$carnac_outdir, carnac outdir
$carnac_predicted_outdir, carnac outdir for predicted RNA
$quiet, the quiet mode
returns : nothing.
The function will execute the masking step on the reference file and the other genomes if there's a genbank annotation file aside.
parameters :
$reference_file, the location of the reference file
$other_files, the reference on the hash table containing other files
$cmd_mask, the command to execute the masking script
$current_mask_outdir, the outdir of masked files
$content_warning, the content of the warning file
$quiet, the quiet mode
returns : nothing.
The function will RNAz on conserved regions found by the previous step.
parameters :
$cmd_rnaz, the command to execute RNAz
$cmd_clustalw, the command to execute clustalw
$cmd_rnazwindow, the command to execute rnazWindow.pl
$cmd_rnaplot, the command to execute RNAplot
$cg_seq_outdir, the outdir of conserved regions
$yass_available, yass software wanted or not
$blast_available, blast software wanted or not
$yass_outdir_name, name of the outdir of yass
$blast_outdir_name, name of the outdir of Blast
$rnaz_outdir, rnaz outdir
$rnaz_predicted_outdir, rnaz outdir for predicted RNA
$quiet, the quiet mode
returns : nothing
The function will execute carnac and/or RNAz on conserved regions found by the previous step.
parameters :
$carnac_available, carnac wanted and usable
$rnaz_available, RNAz wanted and usable
$cmd_carnac, the command to execute carnac
$cmd_rnaz, the command to execute RNAz
$cmd_clustalw, the command to execute clustalw
$cmd_rnazwindow, the command to execute rnazWindow.pl
$cmd_rnaplot, the command to execute RNAplot
$cg_seq_outdir, the outdir of conserved regions
$yass_available, yass software wanted or not
$blast_available, blast software wanted or not
$yass_outdir_name, name of the outdir of yass
$blast_outdir_name, name of the outdir of Blast
$carnac_outdir, carnac outdir
$rnaz_outdir, rnaz outdir
$predicted_outdir, outdir for predicted RNAs
$quiet, the quiet mode
returns : nothing.
The function will execute the alignment step with Yass on the reference against all other files.
parameters :
$reference_file, the location of the reference file
$other_files, the reference on the hash table containing other files
$cmd_yass, the command to execute Yass
$yass_outdir, the outdir of alignment files
$quiet, the quiet mode
returns : nothing.
The function will execute the finding conserved regions step according to alignments (Yass and/or Blast).
parameters :
$reference_file, the location of the reference file
$other_files, the reference on the hash table containing other files
$cmd_cg_seq, the command to execute CGseqcore
$alignments_outdir, the outdir of alignment files
$yass_available, yass software wanted or not
$blast_available, blast software wanted or not
$yass_outdir_name, name of the outdir of yass
$blast_outdir_name, name of the outdir of Blast
$cg_seq_outdir, outdir of conserved regions
$quiet, the quiet mode
returns : nothing.
The function will execute and deal with RNA predicted files from RNAz.
parameters :
$cmd_rnaz, command line to execute RNAz
$cmd_clustalw, command line to execute clustalw
$cmd_rnazwindow, command line to execute rnazWindow.pl
$is_rnazwindow, rnazWindow.pl executable or not
$general_outdir, the outdir for result file
$set_outdir, the outdir for RNA predicted sets
$cg_seq_outdir, the outdir of conserved regions found
$outdir_name, the name of subdirectory
$sets, the reference on conserved regions found to process
returns : the number of sets predicted as RNA.
Benjamin Grenier-Boley <benjamin.grenier-boley@inria.fr>