HextractoR {HextractoR}

HextractoR: Integrated Tool for Hairping Extraction of RNA Sequences

Description

To preprocess a genome, you need a file containing the raw genome in fasta format. To run HExtractor, simply call the main function. This function creates 2 files in the "out" folder and automatically names them.

Usage

HextractoR(input_file, min_valid_nucleotides = 500, window_size = 160,
  window_step = 30, only_sloop = T, min_length = 60, min_bp = 16,
  trim_sequences = T, margin_bp = 6, blast_evalue = 1,
  identity_threshold = 90, nthreads = 4, nworks = 4,
  filter_files = { })

Arguments

input_file

filename of the fasta file to proccess

min_valid_nucleotides

Each input sequence must have this quantity of valid nucleotides (not 'N') to be processed.

window_size

Number of bases in the windows.

window_step

Window step. This number defines indirectly the overlap: window_overlap=window_size-window_step

only_sloop

Only extract single loop sequence.

min_length

Minimum sequence length. Shorter sequences are discarded.

min_bp

Minimum number of base-pairs that must form a sequence.

trim_sequences

Use some heuristics to trim the hairpins.

margin_bp

When the sequence is trimmed, at least min_bp+margin_bp base-pairs are left.

blast_evalue

e-value used in blast to match the extracted sequences with the sequences from the filter files.

identity_threshold

Identity threshold used to match sequences with the sequences from the filter files.

nthreads

Allows using more than one thread in the execution.

nworks

Split each sequence in nworks to use less RAM memory.

filter_files

Fasta files with known sequences to separate the output stems.

Value

A list with the path of the output files and the result of the proccessing of each sequence (if it was succesful or failed)

Examples

# Small example without filter files
library(HextractoR)
# First we get the path of the example FASTA file
fpath <- system.file("Example_tiny.fasta", package="HextractoR")
# To run HextractoR, simply call the main function
HextractoR(input_file = fpath)
# Other example with filter files and bigger input file
fpath1 <- system.file("Example_human.fasta", package="HextractoR")
fpath2 <- system.file("Example_pre-miRNA.fasta", package="HextractoR")
HextractoR(input_file = fpath1, filter_files = {fpath2})
# This function creates 2 files in the working directory and automatically
# names them.