NAME

Package general_functions - General pipeline functions


SYNOPSIS

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

Provided functions :


EXPORT

Exported functions :


FUNCTIONS

create_directory

Create a directory.

erase_existing_files

Erase all existing files and subdirectories under the provided directory

execute_reverse_complementary

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

exit_script

Prints an error message and exit the script

get_info_genbank

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

get_ratio_paired_bases

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

get_reverse_base

Return the complementary base of the provided one.

produce_result_files

The function will create the result files.

read_fasta

Read a fasta file and return its id and sequence.

read_file

Read a file and return its content.

sort_by_num

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

sort_by_pos

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

write_file

Write a content into a file.


AUTHOR

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