parse_blast: parse_blast

Description Usage Arguments Value

View source: R/parse_blast.R

Description

Function to parse xml output of ncbi blast of V3kl V6r regions returns query cover, evalue, percent identity, matched organism(s), accession number, query sequence returns hits in percent identity-coverage groups, starting from the group with the highest scores in both those measures, and in decreasing order

Usage

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parse_blast(filename = NULL, ngroups = 1, tophit = FALSE,
  output = "blast_result.csv")

Arguments

filename

name of xml file containing blast search results for V3klV6r sanger

ngroups

default 1; the number of identity-coverage groups to be returned

tophit

default FALSE; if TRUE, only returns the top hit for each query

output

default 'blast_result.csv'; name of output file; will be in csv format; will be saved in same location as input file.

sequencing

(exported from ncbi blast); full path to file should be included

Value

blast results in the form of csv file, e.g. blast_result.csv


schyen/isolationWorkflow documentation built on May 24, 2019, 2:03 a.m.