• NAME
• SYNOPSIS
• EXPORT
• FUNCTIONS
• create_directory
• erase_existing_files
• execute_reverse_complementary
• exit_script
• get_info_genbank
• get_pos_genes
• get_ratio_paired_bases
• get_reverse_base
• produce_result_files
• read_fasta
• read_file
• sort_by_num
• sort_by_pos
• write_file
• AUTHOR

NAME

Package general_functions - General pipeline functions

SYNOPSIS

Contains all functions to handle configuration files used in the pipeline.

Provided functions :

• create_directory

• execute_reverse_complementary

• exit_script

• get_info_genbank

• get_pos_genes

• get_reverse_base

• get_ratio_paired_bases

• produce_result_files

• produce_result_pipeline

• read_fasta

• read_file

• sort_by_num

• write_file

EXPORT

Exported functions :

• create_directory

• execute_reverse_complementary

• exit_script

• get_ratio_paired_bases

• get_reverse_base

• produce_result_files

• read_fasta

• read_file

• sort_by_num

• sort_by_pos

• write_file

FUNCTIONS

create_directory

Create a directory.

• parameters : $dir, the directory to create

• returns : nothing but the directory is created.

erase_existing_files

Erase all existing files and subdirectories under the provided directory

• parameters : $dir : the directory containing files to erase

• returns : Nothing but all files and subdirectories are erased

execute_reverse_complementary

The function will create the reverse complementary set for all sets provided in the paths.

• parameters :

  • $file, the file to get the reverse complementary

  • $outfile, the outfile to write the complementary file

• returns : nothing but the reversed file is created.

exit_script

Prints an error message and exit the script

• parameters : $message, the error message to print

• returns : nothing but the script exited

get_info_genbank

Get information on genes, RNAs in a genbank file : positions, name, locus, product and strand.

• parameters : $genbank, the genbank file

• returns :

  • $ref_pos, the reference on the positions array

  • $ref_pos_name, the reference on a hash table that links positions and name

  • $ref_pos_locus, the reference on a hash table that links positions and locus

  • $ref_pos_prod, the reference on a hash table that links positions and product

  • $ref_pos_strand, the reference on a hash table that links positions and strand

get_pos_genes

Retrieve positions of the gene located before the pos_start and the positions of the gene located after the pos_end.

• parameters :

  • $pos_start, the prediction starting position

  • $pos_end, the prediciotn ending position

  • $pos, the reference on array containing positions

• returns :

  • $pos_gene_5prime, the positions of the genes located in 5'

  • $pos_gene_3prime, the positions of the gene located in 3'

get_ratio_paired_bases

Get the ratio paired-bases/length sequence in carnac result file for the first sequence only : the reference sequence.

• parameters, $file, the carnac output file ``carnac.out'' to read

• returns, the ratio paired-bases/length sequence.

get_reverse_base

Return the complementary base of the provided one.

• parameters : $base, the base to get its complementary

• returns : the complementary base (or N if unknown)

produce_result_files

The function will create the result files.

• parameters :

  • $reference_file, the reference file location

  • $other_files, reference on array containing other files

  • $mask_coding_available, masking regions step or not

  • $mask_cds_wanted, masking CDSs wanted

  • $mask_rna_wanted, masking RNAs wanted

  • $mask_redundancy_available, masking redundant regions step or not

  • $yass_available, yass alignment step or not

  • $blast_available, blast alignment step or not

  • $cg_seq_available, find conserved regions or not

  • $carnac_available, carnac prediction or not

  • $rnaz_available, RNAz prediction or no

  • $all, all pipeline available or not

  • $yass_outdir_name, the name of yass outdir

  • $blast_outdir_name, the name of blast outdir

  • $rna_predicted_outdir, the location of RNA predictions

  • $outdir, the outdir

  • $warning_file, the warning file if warning occured or ``''

  • $time_diff, the pipeline execution time

• returns : nothing but the result files are created.

read_fasta

Read a fasta file and return its id and sequence.

• parameters : $fasta, the fasta file to read

• returns : the id and sequence or nothing if nto fasta format.

read_file

Read a file and return its content.

• parameters : $file, the file to read

• returns : the content of the file.

sort_by_num

Comparison function used to sort files by their number (Files must have a name like by digits).

• parameters : $a, $b representative of 2 file names

• returns : 1,0 or -1 ($a > $b, $a = $b, $a < $b).

sort_by_pos

Comparison function used to sort sets by their position on the reference sequence

• parameters : $a, $b representative of 2 set names

• returns : 1,0 or -1

write_file

Write a content into a file.

• parameters :

  • $content, the content to write

  • $file, file to write

• returns : Nothing but the file is written.

AUTHOR

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