read.ptt: Read a NCBI protein or RNA feature table

In cstubben/genomes2: Genome sequencing project metadata

Description

Read a protein or RNA table from NCBI genomes ftp.

Usage

read.ptt(file)

Arguments

file	a protein table

Details

Protein and RNA table (*.ptt and */rnt) are available in the NCBI genomes ftp directory at ftp://ftp.ncbi.nih.gov/genomes

Value

GRanges with 6 elementMetadata columns including locus tag id, length (aa), genbank ID, gene name, cog id and product.

Note

Protein tables downloaded from Entrez Genome overview pages have a different format

Author(s)

Chris Stubben

See Also

read.ptt

Examples

  file<-"ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Yersinia_pestis_CO92_uid57621/NC_003143.ptt" 
  x <-read.ptt(file)
  x
  table2(substr(values(x)$cog, 1,7), n=6)

cstubben/genomes2 documentation built on May 14, 2019, 12:25 p.m.