prepare.gb.access: Prepares a set of GenBank Accession IDs for NCBI BLAST...

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

Prepares a set of GenBank Accession IDs for NCBI BLAST submission

Description

Prepares a set of GenBank Accession IDs for NCBI BLAST submission

Usage

prepare.gb.access(GBaccess.bed, ncores = 1)

Arguments

GBaccess.bed	A data.table or a data.frame in a BED-like format containing columns as following: column 1: The Genbank accession IDs column 2: The start position of the sequence to keep column 3: The end position of sequence to keep
ncores	An integer specifying the number of cores or threads to be used for parallel processing.

Value

A list of sequences based on information provided in GBaccess.

Author(s)

Yoann Pageaud.

References

Paradis E. & Schliep K. 2019. ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R. Bioinformatics 35: 526–528. doi:10.1093/bioinformatics/bty633. HAL: ird-01920132.

Examples

#Create example 1 row data.frame
df <- data.frame("GBaccessID" = "AC073318", "Start" = 71401, "End" = 120576)
#Prepare sequence for submission to NCBI BLAST
seq.list <- prepare.gb.access(GBaccess.bed = df)
# seq.list can now be used by submit_NCBI_BLAST

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