processBlastResult: Process Blastn Result

In iferres/quickMLST: Quick Multi Locus Sequence Typing Analisys

Description

Process blastn output. Reports whether the genome contains a reported allele in pubmlst, or it has a not reported (new) allele, or if no allele where found. In case a new allele were found, a fasta file is written.

Usage

processBlastResult(
  blastRes,
  pid = 90,
  scov = 0.9,
  write = "new",
  prefix = "alleles",
  dir = ".",
  dnw = paste0(dir, "tmp/")
)

Arguments

blastRes	A data.frame as returned by readBlastResult.
pid	Percentage identity reporting threshold.
scov	Query coverage reporting threshold.
write	character. One of "new" (Default), "all" or "none". The fist one writes only new alleles found (not reported in pubmlst.org), the second writes all alleles found, and "none" do not write any file.
prefix	character A prefix to the fasta files of found sequences (see write). (Default: "allele").
dir	The directory where to put the fasta file of allele sequences found.
dnw	Temporary directory where to put new alleles to check later if are the same.

Value

The allele number id if an exact match with a reported mlst gene is found, a name arbitrarily given if a new allele is found, or NA if no alleles are found.

Author(s)

Ignacio Ferres

iferres/quickMLST documentation built on Dec. 22, 2020, 5:10 p.m.