MEGAN 6: Could you provide mapping files in plain text format in addition to binary?

User Questions
1

Hi,

I have a couple of question regarding the mapping files for MEGAN 6, like acc2seed-May2015XX.abin.zip.
As far as I know, these files are available in binary format only according to the “User Manual for MEGAN V6.7.11”:

Files ending on .bin are simple binary files for looking up GI to taxon ids. The taxon id associated with a given GI number n is located at position 4n in the file.
Files ending on .abin represent a disk-based hash table that maps accession numbers (such as NP_660210) to taxon ids.

Would it be possible to upload these files in plain text format as well, so they could be analysed outside of MEGAN?

Also, > Note that the SEED ids used by MEGAN are not official ids.
What was the reason for that decision and is it possible for you to provide a file mapping MEGAN’s SEED IDs and original SEED IDs?

Thank you.

2

MEGAN’s SEED mapping files are quite out of date (last updated May 2015).
Unfortunately, the SEED functional classification appears to be a closed system and the providers of SEED do not provide public access to the mapping of accessions to SEED functional roles. So there is no way for us to update this mapping file.

My understanding is that there are no “original SEED IDs”, that is, there is nothing comparable to e.g. KO ids in KEGG.

3

Thank you, Daniel. So, the latest SEED mapping file in plain text format will be the gi2seed.map.gz for MEGAN5 of 1 Nov 2014? Would it be possible to make the SEED mapping file acc2seed-May2015XX.abin.zip (I assume this is the latest version of May2015) available in plain text format as well? It would be really helpful for direct comparisons of MEGAN’s annotations to ones made by other programs.

4

Would you have text-based accession mappings for the other databases (Interpro, EggNOG, etc) available, or could you point out where would be the best place to grab them?

Also, I have the latest UE release (6.7.18), and I have been getting this error with the interpro tool:

[cjfields@biologin-0 tools]$ ./interpro/make-acc2interpro
Error: Could not find or load main class megan6u.tools.interpro2go.MakeAccToInterProMap

This doesn’t happen with the other tools, where I get a help menu.

5

Thanks for the bug report, I found the problem and it will be fixed in the next update

6

I will look into providing all mapping files in text format.

7

Thank you for that, Daniel.

8

Agreed, thanks Daniel!

9

Hello Daniel.

Is the acc2interpro mapping currently available in text format?

10

We are working on changing the way mapping files are shipped. In the new solution, all maps will be shipped as a single sqlite database. This will provide access to all mappings.

3 Likes