Reading FASTA file with multiple sequences

Question

[Seot]

Hello all,

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”)

contigs_dna= contigs[[1]]   (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(contigs_dna, sens = "F", NAstring = "X", ambiguous = FALSE, frame = 0, numcode = 1)

contigs_aa= getTrans(contigs_dna,sens = "F")    

write.fasta(contigs_aa,contigs_aa,file.out = "contigs_aa.fasta")

contigsaafile = read.fasta("contigs_aa.fasta", seqtype = "AA")

getAnnot(contigsaafile)

[shenwei356]

use loop to handle all the contigs

[WouterDeCoster]

Hello Seot!

It appears that your post has been cross-posted to another site: https://support.bioconductor.org/p/92193/

This is typically not recommended as it runs the risk of annoying people in both communities.