transcript/subsystems

Code for making bioinformatics work with the SEED subsystems database a little easier.

subsystems's Issues

Issue in making a subsystems.complex blast searchable db using makeblastdb

Hi,

I am trying to use your discoveries and work (thanks) to make a blast searchable database of the SEED subsystems.

By only using the simplifier script on subsystem.complex the resulting FASTA gives me issues; if I use makeblastdb with the option -parse_seqids (which I need to use) it tells me that there are duplicate IDs. Tried removing duplicates, but the error persists. I think makeblastdb does not like the way these IDs are formatted.

The error:

BLAST Database creation error: Error: Duplicate seq_ids are found:
GNL|FIG|66692.3.PEG.217

P.S. Also, after using your simplifier script you also need to run this:
sed -i '1d' subsystems.complex.modified && sed -i '$ d' subsystems.complex.modified

Because there is a line at the beginning and one empty at the end, both cause problems with makeblastdb.

On the other side, the rebuilder script creates more complete IDs but they also cause issues with makeblastdb.

I would like to ask you if you actually made a blast searchable database using makeblastdb out of this, and if so, if you could quickly explain the step that you took.