BXD: A list to identify the Blast fields to retrieve.

In BigelowLab/blastxml: Extract data from Blast XML files

Description

blastn includes... Iteration_iter_num Iteration_query_id Iteration_query_def Iteration_query_len Hit_num Hit_id Hit_def Hit_accession Hit_len Hsp_num Hsp_bit_score Hsp_score Hsp_evalue Hsp_query_from Hsp_query_to Hsp_hit_from Hsp_hit_to Hsp_query_frame Hsp_identity Hsp_positive Hsp_gaps Hsp_align_len Hsp_qseq Hsp_hseq Hsp_midline

Usage

BXD(x = "blastn", fields = NULL)

Arguments

x	character by default the fields are for 'blastn' but this is set automatically when the file is opened. Alternatively, this can be the xml filename.
fields	character of NULL if not NULL fields are subset to include just these. The default can be found using get_BXD_names()

Value

a named list of fields to return

• app the name of the blast application by default 'blastn'

• blastn a list of character vectors fields in for Iteration, Hit and Hsp

BigelowLab/blastxml documentation built on May 5, 2019, 2:42 p.m.