extract_regions_from_fasta: Extract regions from a fasta file

In joelnitta/baitfindR: Find Baits for Sequence Capture

Description

Wrapper for bedtools getfasta.

Usage

extract_regions_from_fasta(bed_file, fasta_file, out_fasta_file, ...)

Arguments

bed_file	Path to bed file with locations of regions to extract. bed file is a tab-separated file with columns for chromosome (e.g., chr1), start position (e.g., 1), and end position (e.g., 10), in that order. No column headers are used.
fasta_file	Path to file in fasta format to extract regions from.
out_fasta_file	Path to write extracted regions (in fasta format).
...	Other arguments. Not used by this function, but meant to be used by drake_plan for tracking during workflows.

Value

List; output of processx::run(). Externally, a fasta file will be written to the path specified by 'out_fasta_file'.

Author(s)

Joel H Nitta, [e-mail]

Examples

## Not run: 
# First write gene, intron, and exon bed regions out as tsv files

temp_dir <- tempdir()

find_bed_regions(
  gff3_file = system.file("extdata", "Arabidopsis_thaliana_TAIR10_40_small.gff3",
  package = "baitfindR", mustWork = TRUE),
  source_select = "araport11",
  out_type = "write_all",
  out_dir = temp_dir,
  prefix = "arabidopsis"
)

# Extract genes.
extract_regions_from_fasta(
  bed_file = fs::path(temp_dir, "arabidopsis_introns"),
  fasta_file = system.file("extdata", "Arabidopsis_thaliana_TAIR10_40_small.fasta",
  package = "baitfindR", mustWork = TRUE),
  out_fasta_file = fs::path(temp_dir, "arabidopsis_gene_seqs.fasta")
)

## End(Not run)

joelnitta/baitfindR documentation built on May 7, 2020, 6:21 p.m.