parse_blast: parse_blast

In schyen/somefxns: Generic Tools to Help with Analysis

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

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

Value

csv file with blast results

schyen/somefxns documentation built on Aug. 6, 2019, 2:26 p.m.