read a fasta file and gets amino acid composition for all proteins then writes to csv

aa_comp.R

library(Peptides)
library(seqinr)

get_comp <- function(fasta){
  s=getSequence(fasta, as.string = TRUE);
  sname=getName(fasta);
  
  comp = aaComp(s);
  
  r<-c(name=sname,
       tiny=comp[[1]][1,2], 
       small=comp[[1]][2,2], 
       aliphatic=comp[[1]][3,2],
       aromatic=comp[[1]][4,2], 
       nonpolar=comp[[1]][5,2], 
       polar=comp[[1]][6,2],
       charged=comp[[1]][7,2],
       basic=comp[[1]][8,2],
       acidic=comp[[1]][9,2]);
  
  return(r);
}


fastas = read.fasta("all_sequences.fasta")

compositions_list=lapply(fastas, get_comp)

df_res = data.frame(t(sapply(compositions_list,c)))

write.table(df_res,"compositions.csv", sep = ";", row.names = FALSE, col.names = TRUE)