TheAlgorithms/R

Multiple sequence alignment using R

shreejyoti opened this issue · 9 comments

shreejyoti commented

myAlignment<- msaClustalW("mydata", type = "dna")
use default substitution matrix
Error in convertAlnRows(result$msa, type) : There is an invalid aln file!

I'm facing issue using the above code. I want to perform multiple sequence alignment on csv or fasta file. but getting this error. please help me to solve it.

Preetiraj3697 commented

!assign

Preetiraj3697 commented 
library(Biostrings)

#Set the file path and name
file_path <- "mydata.fasta"

# Perform the multiple sequence alignment using ClustalW
myAlignment <- msaClustalW(file_path, filetype = "fasta", type = "dna")
siriak commented

@Preetiraj3697 please create a PR with the fix

Preetiraj3697 commented

@siriak How to create a PR

siriak commented

@shreejyoti this doesn't look like code from this repository, so it doesn't need to be fixed. Please see @Preetiraj3697's answer

shreejyoti commented

Thank you for solving!

oliver7423 commented

hi i hope this thread is online.

i have the same problem and this is my coding

AlignNeeded = TRUE # The program reads fasta file and aligns it
if (AlignNeeded) {

file <- readDNAStringSet(fname)#for reading multiple DNA sequences from msa package
file
}

cb<- msa(file) # multiple sequence alignment from msa package
cb

Error in convertAlnRows(result$msa, type) : There is an invalid aln file!

Idk what to do

oliver7423 commented

hi i hope this thread is online.

i have the same problem and this is my coding

AlignNeeded = TRUE # The program reads fasta file and aligns it if (AlignNeeded) {

file <- readDNAStringSet(fname)#for reading multiple DNA sequences from msa package file }

cb<- msa(file) # multiple sequence alignment from msa package cb

Error in convertAlnRows(result$msa, type) : There is an invalid aln file!

Idk what to do

btw this is from R studio