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_000775 700 124 236
CTAACCTCTCCCAGTGTGGAACCTCTATCTCATGAGAAAGCTGGGATGAG

>NM_003820 700 111 222
ATTTCCTCCTGCTGCCCGGGAGGTAACACCCTGGACCCCTGGAGTCTGCA

Questions:

1) How can I read this fasta file into R as a dataframe where each row is a sequence record, the 1st column is the refseqID and the 2nd column is the sequence.

2) How to extract subsequence at (start, end) location?

NM_000016 1  3 #"ACA"
NM_000775 2  6 #"TAACC"
NM_003820 3  5 #"TTC"

score 18 · Accepted Answer · answered Jan 21 '14 at 16:33

18

You should have a look at the Biostrings package.

library("Biostrings")

s = readDNAStringSet("nm.fasta")
subseq(s, start=c(1, 2, 3), end=c(3, 6, 5))

answered Jan 21 '14 at 16:33

sgibb

23,631
1
59
67

1

This function is masking the repeats. How do we prevent that? – DarkRose Jul 12 '16 at 17:31
Can you give a little example? Maybe ask on https://support.bioconductor.org/ for specific use cases. – sgibb Jul 15 '16 at 09:26
Oh, thank you :) I solved the problem using Python. Just treated them as strings. I wanted to delete those sequences which had repeats. So, I used string.isupper() to check that. – DarkRose Jul 18 '16 at 07:58
I kind of have the same question regarding the masking: `DNAString("TATCAAATACTCAAGCACtaaggaaacaggaaaatct")` will return `37-letter "DNAString" instance seq: TATCAAATACTCAAGCACTAAGGAAACAGGAAAATCT` Why is `aaggaaacaggaaaatct` not staying in lowercase? – M. Beausoleil Nov 10 '17 at 18:18

score 12 · Answer 2 · answered Sep 24 '15 at 21:00

12

library("Biostrings")

fastaFile <- readDNAStringSet("my.fasta")
seq_name = names(fastaFile)
sequence = paste(fastaFile)
df <- data.frame(seq_name, sequence)

answered Sep 24 '15 at 21:00

lblum

143
1
5

1

could you please explain your answer – Prudhvi Sep 24 '15 at 21:18

score 3 · Answer 3 · edited Sep 04 '15 at 12:03

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)

Read FASTA into a dataframe and extract subsequences of FASTA file

3 Answers3

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