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,
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written
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helene.cecilia3 •
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
Thank you! However, when I try this it says that cat ended its execution with signal 13, do you know what it means?
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written
by
helene.cecilia3 •
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