I'm trying to read a fasta file that has over 5000 sequences. The plan is to create a vector that calls out all the sequences, and those sequences I'll carry over to Bio Linux after I turn them into protein. I've done this, but with only one sequence at a time (that and I'm still new to RStudio). Please see below for the codes I'm using... Can someone please tell me where I'm going wrong?
> contigs= read.fasta("contigs.fasta", seqtype = “DNA”)
> contigsdnaseq= contigs[] (I think this is the part where things go wrong. I'm not sure what code to use in order for the program to recognize the 5000+ sequences.)
> getTrans(contigsdnaseq, sens = "F", NAstring = "X", ambiguous = FALSE, frame = 0, numcode = 1)
> contigs_aa= getTrans(contigsdnaseq,sens = "F")
> write.fasta(contigs_aa,contigs_aa,file.out = "contigs_aa.fasta")
> contigsaafile = read.fasta("contigs_aa.fasta", seqtype = "AA")