Read FASTA into a dataframe and extract subsequences of FASTA file

Question

I have a small fasta file of DNA sequences which looks like this:

>NM_000016 700 200 234
ACATATTGGAGGCCGAAACAATGAGGCGTGATCAACTCAGTATATCAC

>NM         


        

Answer 1

inspired by sgibb's answer above, I answer the first question as follow:

#read fasta file into R as a dataframe: 1st column as "RefSeqID", 2nd column as "seq"

library("Biostrings")
fasta2dataframe=function(fastaFile){
s = readDNAStringSet(fastaFile)
RefSeqID = names(s)
RefSeqID = sub(" .*", "", RefSeqID) 
#erase all characters after the first space: regular expression matches a space followed by any sequence of characters and sub replaces that with a string having zero  characters 

for (i in 1:length(s)){
seq[i]=toString(s[i])
}

RefSeqID_seq=data.frame(RefSeqID,seq)
return(RefSeqID_seq)
}

Example:

mydf = fasta2dataframe(myFastaFile.fasta)