Concatenate Two .Fasta Files Into One

Question

[Alice]

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.

[Biojl]

Could you comment on the rationale behind what you're trying to do?

[Alice]

In few words: concatenated sequence matrix -> alignment -> phylogenetic tree

[Ashutosh Pandey]

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

[Alice]

No, it's for my lab work. Your answer is also helpful, thanks.

Answer 1

[Devon Ryan]

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.

[Alice]

I've already tried that. Error: the 'cbind' method for "DNAbin" accepts only matrices

[Devon Ryan]

How did you read in the sequences?

[Alice]

read.dna("B.fa", format="fasta") - fail read.FASTA("B.fasta") - fail

[Devon Ryan]

If you get an error message of "fail" or something like that, then you have bigger issues.

[Alice]

by "fail" i mean the same error message in both cases: cbind' method for "DNAbin" accepts only matrices

[Devon Ryan]

It would be helpful if you posted a reproducible example. The original examples in your question will work fine.

[Alice]

I think problem is in lines, i.e. one sequence is like:

>sp1
aattgg
aaggtt

and not

>sp1
aattggaaggtt

[pescadordigital]

Worked for me.

Answer 2

[Haluk]

You can do this with an awk

paste A.fa B.fa | awk '{if (NR%2==0) {print $1 $2} else {print $1}}'

[Alice]

Thank you! It works. I have absolutely no experience with awk, so i have one question: the order of IDs in A.fa have to be the same, as in B.fa? Or concatenation goes by comparing IDs in two files?

[Devon Ryan]

They have to be the same and each sequence can occupy only 1 line.

[Alice]

Ok, thanks, it is really important.

[Ashutosh Pandey]

paste -d '\0' File_A File_B | sed 's/>[A-Z]*//' > File_C.fa will also do the same.