How do concatenate different fasta file

Question

[lkianmehr]

Does anybody know what is the best and trustable way to concatenate different FASTA files for making them index together?

thanks in advance

[nadiawerksfoon]

How do i delete all the fasta files with my info

[Ram]

Please ask a new question and give us as much information as you can. Do not add an answer unless you're answering the top-level post. I'm moving your "answer" to a comment and deleting the other duplicate "answer".

[ATpoint]

give us as much information as you can

In this it would be "please give any information"...

nadiawerksfoon imagine you were in the situation of a user reading this and willing to help, could you reproduce at all what the problem is? At least I cannot. Probably others cannot as well. Add details!

Answer 1

[GenoMax]

Just cat them together. I am not sure what you mean by trustable?

If you have spaces in the headers (e.g. words separated by names) make sure to change the space to _. Most aligners will drop things past first space when reporting alignments (e.g. bbmap is an exception and will keep the entire name by default unless you use trd=t). You may get confusing results if the part of name up to first space is common to more than one record.

Answer 2

[Nicolas Rosewick]

As Genomax commented :

In a unix shell :

cat file1.fasa file2.fastq file3.fasta > merged_file.fasta

or even easier if all your fasta files are in a directory and ends by .fasta

cat *.fasta > merged_file.fasta

[ATpoint]

I tend to remember that there were cases (also reported here on Biostars) when cat *.fasta somehow caused an infinity loop because the output file would be constantly appended to itself (as it also ends on .fasta). To avoid this, consider to use:

find . -maxdepth 1 -name \*.fasta | xargs cat > output.fasta

[Nicolas Rosewick]

that's a good point !