list to one fasta file
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Entering edit mode
3.9 years ago
c.chakraborty ▴ 170

Dear all,

I used biomaRt to retrieve the 3'UTR sequences of 1527 transcpts, using their refseq ids:

for (i in uniquetrans[,1]) {
sequences[i] = getSequence(id = i,type = "refseq_mrna",seqtype = "3utr", mart = ensembl, verbose = FALSE)
}


The sequences were retrieved, but now, I have a problem in converting the list into a file. I tried exportFASTA(), but it works for a single sequence at time which is irritating. I also tried lapplys such as

 lapply(sequences, write, "test.txt", append=TRUE, ncolumns=1527)


and I got the sequences, but they don't have a header. What do i do now. I can write a for loop and convert each one in a separate text file, but it is so cumbersome! Please help.

Regards,
Chaitali

R biomaR FASTA • 1.2k views