read FASTA file in R, including description information

Question

[friasoler]

Hello everybody

I'm trying to import a: *.fna file, in R, and I have no idea how to deal with it. I would need to have columns like these: Isogroup, Contigs, Length, Sequence. As one Isogroup contain more that one Contig they will be repeated; but that is exactly what I want. I will appreciate your help. An example file is included. They have paragraph tab after each line.

Regards
Roberto

>contig00002 gene=isogroup00001 length=656
CTAATCCTCAAACCCGAACTCATCTCAGGCCTCCCTATATGCAAGTATAGTTTCAACCCA
CTCCCCACACCATCAAACATCTCAGCTTGATGAAATTTCGGGTCATTACTGGGCATTTGC
>contig00004 gene=isogroup00001 length=566
CACAGATACAGATGGTTGGGGATGCAACAGTCCTCATCCTACTTCGTAATCGCGGCATTC
>contig00005 gene=isogroup00001 length=1152
CTCCCCACACCATCAAACATCTCAGCTTGATGAAATTTCGGGTCATTACTGGGCATTTGC
>contig00007 gene=isogroup00001 length=547
AACCCAACCAAAGCATTTGCCAGTCCCAGTATAGGCGATAGAAAAGACACCATTGGAGCG
>contig00008 gene=isogroup00001 length=698
AaGGgGGGGGggTGGTTCTCGTAGTTAAATGCTTATAACAGtGGCTTTTCAGGCCGTTGA
>contig00024 gene=isogroup00001 length=2170
CTTGGACGCTCTATTATCCCGTGTGAATCATCCCGTCGTCATTTGTCGGGGCTGGGAGAG

Answer 1

[Erik Wright]

You could use the readDNAStringSet function in the Biostrings package:

library(Biostrings)
dna <- readDNAStringSet("<<PATH TO FASTA FILE>>")
s <- strsplit(names(dna), "[ \t]+") # split names by tab/space
info <- matrix(unlist(s), ncol=3, byrow=T)

More text parsing may be added as desired. Hope that helps!

[friasoler]

Thanks Erik. I have got something but I can not get the sequence along the row with the isogroup, contig information. Sorry I can't get the sequences beside the Contig information

Answer 2

[Sean Davis]

Check out the readFASTA() method in the Biostrings Bioconductor package. Some postprocessing will be needed to get a data.frame with the columns as you describe.