[Seqinr-forum] extract A/C/G/T positions in a FASTA file

[jiehuang001 at gmail.com]

Hi, guys:

 

Previously I have been using library(Biostrings).  

For example, I have used the following 2 lines to read in a SARS-COV-2 FASTA
file and find the positions for all "A" allele.

fa <- readDNAStringSet("MY-FASTA.fa", format="fasta")

I could then use vmatchPattern("A", fa, max.mismatch=0)

 

However, the output from the above vmatchPattern() command is a bit messy. 

 

I wish that SeqinR package could do this more straight-forward.

If so, can someone please let me know how to write my above Biostrings
command for SeqinR?

 

Thank you very much & best regards,

Jie

 

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