RetrivingSeqs.md

Example how to pull out sequences from the NCBI_ClassifiedSeqs.tsv

You will need some familiarity with R, and the packages tidyverse and Biostrings are needed.

Load packages and the file

library(tidyverse)
library(Biostrings)

NCBI_ClassifiedSeqs = read_delim("NCBI_ClassifiedSeqs.tsv", 
    delim = "\t", escape_double = FALSE, trim_ws = TRUE)

This will give you a df with ONLY Microcystis

Microcystis = NCBI_ClassifiedSeqs %>% 
  filter(Genus == "Microcystis")

This will give you a df with the family Microcystaceae

Microcystaceae = NCBI_ClassifiedSeqs %>% 
  filter(Family == "Microcystaceae")

This will give you a df with the order

Chroococcales = NCBI_ClassifiedSeqs %>% 
  filter(Order == "Chroococcales")

Save the file

This saves as a fasta file with the Genbank accession number and name

Microcystis = Biostrings::DNAStringSet(Microcystis$Sequence)
names(Microcystis) = paste(Microcystis$Genbank_accession)
Biostrings::writeXStringSet(Microcystis, "Microcystis.fasta")