export_geneNt_fasta {GenBank} R Documentation

export gene fasta from the given genbank assembly file

Description

Usage

export_geneNt_fasta(gb,
    title = ".  |",
    key = ['CDS'],
    required = NULL,
    unique.names = FALSE);

Arguments

gb

[as File]

title

[as string]

unique.names

[as boolean]

Details

fasta title is build with a string template, there are some reserved template keyword for this function:

  1. ncbi_taxid - is the ncbi taxonomy id that extract from the genbank assembly

  2. lineage - taxonomy lineage in biom style string, which is extract from the genbank assembly its source information

  3. gb_asm_id - the ncbi accession id of the genbank assembly

  4. nucl_loc - the nucleotide sequence location on the genomics sequence

about the salmon duplicated id error

if you encounter this error while build sequence index by using salmon tool, please set the unique.names parameter to TRUE 

 counted k-mers for 110000 transcripts[2026-01-06 15:08:42.160] [puff::index::jointLog] [error] In FixFasta, two references with the same name but different sequences: AM295250.SCA_1840. We require that all input records have a unique name up to the first whitespace (or user-provided separator) character.

Authors

seqtoolkit

Value

this function returns data object of type FastaFile.

clr value class

Examples

[Package GenBank version 1.0.0.0 Index]