find_in_fasta: R wrapper to ssearch

In jspaezp/jspputils: Series of utilities to interface R with proteomics data analysis

Description

Generates a temporary fasta file with the sequences provided and returns the matches in the provided fasta file.

Usage

find_in_fasta(sequences, target_fasta, ssearch_exe, seq_names = NULL,
  min_eval = 0.01)

Arguments

sequences	sequences to be searched
target_fasta	path to fasta file containing the target sequences
ssearch_exe	location of the ssearch executable (or alias in your path)
seq_names	optional names to be given to the sequences
min_eval	minimum E value to be reported, defaults to 0.01

Details

It wraps sseach to do the search and then returns the console output

Value

tabular console output of ssearch as a character vector (element per line)

Examples

find_in_fasta(c('PEPTIDE'), 'arabidopsis.fasta', '~/usr/bin/ssearch36')

jspaezp/jspputils documentation built on May 23, 2019, 2:50 p.m.