Hi,
I am comparing results from blast/Megan with metaphlan2 and some species show up only in one of them. So I now want to check if those species are actually in the database but can’t figure out how to check what is in the nucl_acc2tax-Mar2018.abin file. How can I convert the .abin file to plain text to see whta is actually in there?
Thank you!
Dear Vanessa,
the file is a binary version of this file:
ftp://ftp.ncbi.nih.gov/pub/taxonomy/accession2taxid/nucl_gb.accession2taxid.gz
which I downloaded in March 2018.
So, you could download and look into that text file.
Here is another idea:
to query the file nucl_acc2tax-Mar2018.abin about specific taxa, you can do the following:
Make a fake CSV import file in the following format:
taxon-name,1
taxon-name,1
…
Here, taxon-name is the name of a taxon you are interested in whereas the “1” is a fake count.
Use the menu item “File->Import->Text (CSV) Format” to import your fake file and you will see which names appear and which don’t.
Example: Contents of file fake.txt:
Fimbriimonas ginsengisoli Gsoil 348,1
Armatimonadetes bacterium,1
Chthonomonas sp. UBA6659,1
Chthonomonas sp. XXXXXX,1
Result:
Here you see that the made-up organism name Chthonomonas sp. XXXXXX does not appear (but rather, the entry is reported as Chthonomonas)
Thanks a lot for the fast and useful reply!
