Combine two FASTA files

[Calico]

I have a couple of fasta files I want to combine, two and two. They're >1 GB so reading them in R is too time consuming. I'm running a Mac on which I can't get Biopython to work and I don't find any tool for this specific purpose on Galaxy.

Does anybody have any suggestion/solution for my problem?

[vivek_]

Can't you just concatenate the two files using cat if there are no duplicates?

[maubp]

I was also going to suggest the command line tool cat, e.g.

cat file1.fasta file2.fasta > combined.fasta

Biopython should work fine on the Mac - using the Apple provided Python, the Python.org version, etc. Please seek help on our mailing list, or start a new thread here.

http://biopython.org/wiki/Mailing_lists

[Calico]

vivek_: Thanks, that worked quite beautifully. I would never have expected the solution to be that trivial.

maubp: Yes, Biopython should work but it's not too easy to install NumPy and SciPy properly, I've found. I'm no terminal wizz.

[maubp]

Biopython doesn't need SciPy, and (on some versions of Mac OS at least) NumPy is already provided by Apple (although not the latest version). You can also install Biopython without NumPy (thins like PDB 3D structures won't work).

[SONIC]

Hi Calici

Try SeqNinja from DNASTAR
www.dnastar.com