Hello, biostars! I have two fasta files for two different genes and want to create one data matrix. Is there any function in R for that? F.ex. if I have 2 DNAbin objects for that genes. Id numbers are identical in both files. I have the first file:
>sp1
aacc
>sp2
ggtt
the second file:
>sp1
ggaa
>sp2
ttgg
I want:
>sp1
aaccggaa
>sp2
ggttttgg
Python is also OK, but i'm interested in R.
2 answers
Just cbind(A,B) to merge the sequences for DNAbin A and DNAbin B:
A.fa:
>sp1
aacc
>sp2
ggtt
B.fa:
>sp1
ggaa
>sp2
ttgg
In R using DNAbin (as you requested):
library(ape)
A <- read.dna("A.fa", format="fasta")
B <- read.dna("B.fa", format="fasta")
C <- cbind(A,B)
write.dna(C, "C.fa", format="fasta")
C.fa:
>sp1
aaccggaa
>sp2
ggttttgg
See help(DNAbin) for more details about options for cbind(), particularly fill.with.gaps and check.names.
How did you read in the sequences?
If you get an error message of "fail" or something like that, then you have bigger issues.
It would be helpful if you posted a reproducible example. The original examples in your question will work fine.
Worked for me.
•
written
by
pescadordigital •
They have to be the same and each sequence can occupy only 1 line.
paste -d '\0' File_A File_B | sed 's/>[A-Z]*//' > File_C.fa will also do the same.
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Could you comment on the rationale behind what you're trying to do?
In few words: concatenated sequence matrix -> alignment -> phylogenetic tree
Is it some kind of homework question. I answered the same question 4-5 days back. See ehre: C: Combining dna sequences files into one
No, it's for my lab work. Your answer is also helpful, thanks.