split_queries.df: Splits a data.frame of Genbank IDs and intervals into a...

In YoannPa/NCBI.BLAST2DT: Submit DNA sequences to NCBI BLAST and get results in an R data.table.

Splits a data.frame of Genbank IDs and intervals into a data.table of smaller intervals.

Description

Splits a data.frame of Genbank IDs and intervals into a data.table of smaller intervals.

Usage

split_queries.df(df, by = 7000)

Arguments

df	A data.frame or a data.table in a BED-like format following the same specifications as 'GBaccess.bed' in prepare.gb.access.
by	An integer to specify the length of the output DNA sequences you wish your queries to be splitted into, in base pair (Default: by = 7000).

Value

A data.table of the Genbank IDs with intervals of the specified length. You can then subset the intervals of interest before submitting the data.table to prepare.gb.access or get.NCBI.BLAST2DT.

Author(s)

Yoann Pageaud.

Examples

#Using an example data.frame of 1 Genbank ID
split_queries.df(
  df = data.frame("GB.access" = "AC073318", "Start" = 71401, "End" = 120576),
  by = 7025)

YoannPa/NCBI.BLAST2DT documentation built on July 1, 2023, 1:03 a.m.