extractSequences: Utility function for extracting sequences from HMMer outputs

In carolinafishes/toast: Transcriptome Ortholog Alignment Sequence Tools

Utility function for extracting sequences from HMMer outputs

Description

This function uses a table of sequence hits and target transcripts parsed from HMMer outputs to extract sequences

Usage

extractSequences <- function(input_csv, type = "AA", external=TRUE) 

Arguments

input_csv	The path to a csv file or the name of a dataframe in memory from which to extract the sequences and header
type	AA for amino acid or DNA for nucleotide
external	Whether or not input_csv is a path to an external file. Default is TRUE. Use FALSE if you wish to run this function on a dataframe

Value

Returns a fasta in the working directory

Author(s)

Alex Dornburg, [e-mail]

Examples

extractSequences <- function(input_csv="filepath/yourcsv.csv", type = "AA", external=TRUE) 

#or if internal and you have this in a dataframe already

extractSequences <- function(input_csv=results, type = "AA", external=FALSE) 

carolinafishes/toast documentation built on Dec. 19, 2024, 12:47 a.m.