Handle directories downloaded from NCBI for database creation

Question

[helene.cecilia3]

Hello,

I want to create a viral database on my computer. I downloaded all the complete viral genomes from ncbi's ftp, the all.fna.tar.gz.

I uncompressed it, and it made thousands of directories, each containing the fasta file(s) for one virus.

I would like to concatenate all these files into one before using formatdb, but I don't know how to do, in python or bash, to go through all the directories and all the files and write all of them in a new one (with cat or something else).

Thank you,

Answer 1

[Pierre Lindenbaum]

makeblastdb can read from stdin:

find /path/to/dir -type f -name "*.fa" -exec cat '{}' ';' |\
path/to/ncbi/ncbi-blast-2.2.28+/bin/makeblastdb  -dbtype nucl  -in -  -out dbName -title dbName

[helene.cecilia3]

Thank you! However, when I try this it says that cat ended its execution with signal 13, do you know what it means?

Answer 2

[5heikki]

tar zxvf all.fna.tar.gz --strip=2

Should extract all the files to the wd.