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

the File ncbi genbank assembly object for export its gene nucleotide sequence data. [as File]

title

the fasta headers title template string for export of the gene sequence data. [as string]

key

the feature key name for extract the gene sequence data, example as gene or CDS.

required

a character vector of the template keyword name for filter the gene export: the gene that its template data is missing any of the required keyword will be skipped. [as string]

unique.names

processing the possible duplicated header as unique id, this option is usually when you use this function for build a sequence database for salmon tool. [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

a FastaFile gene nucleotide sequence collection object.

clr value class

Examples

[Package GenBank version 1.0.0.0 Index]