I have about 100 bacterial species. I used "reutils" package to download their fasta files. I am now trying to download their gff files. I have the name and NC_ ids for these.
I looked online and see that that there is package "genomes" that can read the file into R, but you need to provide the complete link to it . Eg: file<-"ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Yersinia_pestis_CO92_uid57621/NC_003132.gff"
If the link had been something like "ftp://ftp.ncbi.nih.gov/genomes/Bacteria/NC_017105.gff", it would have been easy to programmatically create the link in R and download the file. But that is not the case, since there is a species name and another number in it.
1) Is there an "retuils" type package where I can give the NC_ id and download the gff file ?
2) Is there a way to create this link programmatically for each bacteria ?
Any insights ? Thanks