get_seqs: Gets sequences from bam file

In compbiomed/MetaScope: Tools and functions for preprocessing 16S and metagenomic sequencing microbiome data

Gets sequences from bam file

Description

Returns fasta sequences from a bam file with a given taxonomy ID

Usage

get_seqs(id, bam_file, n = 10, quiet, NCBI_key = NULL, bam_seqs)

Arguments

id	Taxonomy ID of genome to get sequences from
bam_file	A sorted bam file and index file, loaded with Rsamtools::bamFile
n	Number of sequences to retrieve
quiet	Logical, whether to print out more informative messages. Default is FALSE.
NCBI_key	(character) NCBI Entrez API key. optional. See taxize::use_entrez(). Due to the high number of requests made to NCBI, this function will be less prone to errors if you obtain an NCBI key.
bam_seqs	A list of the sequence IDs from the bam file

Value

Biostrings format sequences

compbiomed/MetaScope documentation built on April 1, 2024, 5:35 p.m.