grab_fasta: read in a fasta file and turn into a tibble

In eriqande/snps2assays: Prepare SNP Assay Orders from ddRAD or RAD Loci

Description

This reads in a fasta file and removes the leading ">" from the name of the contig so that it will match stuff in a corresponding VCF or other variant file. It then returns a tibble with columns CHROM and consSeq. Currently this only woks on files that have two line for each sequence, not with files that break the sequence over multiple lines.

Usage

grab_fasta(path)

Arguments

path	The path to the fasta file. If it is gzipped, it will automatically be gunzipped on the fly.

Examples

grab_fasta(system.file("textdata", "fasta.txt.gz", package = "snps2assays"))

eriqande/snps2assays documentation built on Oct. 9, 2020, 5:22 p.m.