get_multi_seqs: Gets multiple sequences from different accessions in a bam...

View source: R/metascope_blast.R

get_multi_seqsR Documentation

Gets multiple sequences from different accessions in a bam file

Description

Returns fasta sequences from a bam file with given taxonomy IDs

Usage

get_multi_seqs(ids_n, bam_file, seq_info_df, metascope_id_tax, sorted_bam_file)

Arguments

ids_n

List of vectors with Taxonomy IDs and the number of sequences to get from each

bam_file

A sorted bam file and index file, loaded with Rsamtools::bamFile

seq_info_df

Dataframe of sequence information from metascope_blast()

metascope_id_tax

Data.frame of taxonomy information

sorted_bam_file

Filepath to sorted bam file

Value

Biostrings format sequences


compbiomed/MetaScope documentation built on Nov. 20, 2024, 8 p.m.