Hello,Sorry, but we had some untested code changes to MicrobeDB just
recently that caused problems. I have fixed the bugs in the current
version of MicrobeDB. You should update MicrobeDB using the
information here:
https://github.com/mlangill/MicrobeDB/blob/master/information/UPDATE/UPDATE.mdThe NCBI_completegenomes.txt file is produced when the
download_version.pl script is run.

If you are trying to test your installation you can do so with this command:
./download_load_and_delete_old_version.pl -d ~/Downloads/ -s ‘-s
Pseudomonas_aeruginosa_LES’

Programming with the MicrobeDB API

• If you know how to program in Perl you can use the MicrobeDB Perl API which allows you to retrieve data without constructing MySQL queries.
• Example of a simple perl script using the MicrobeDB API that searches for all ‘recA’ genes and prints them in ‘Fasta’ format:

  #Import the MicrobeDB API use lib '/your/path/to/MicrobeDB'; use MicrobeDB::Search; #intialize the search object $search_obj= MicrobeDB::Search(); #create the object that has properties that must match in the database $gene_obj= MicrobeDB::Gene(gene_name => 'recA'); #do the actual search @genes = $search_obj->object_search($gene_obj); #loop through each gene we found and print in FASTA format foreach my $gene (@genes){ print'>',$gene->gid(),"\n",$gene->gene_seq(),"\n"; } 

• See more examples using the MicrobeDB API in information/example_scripts.

Extending MicrobeDB

• MicrobeDB can be extended to include additional types of custom information
• The best way to extend MicrobeDB is to create your own tables with the fields of your choice and use a stable NCBI based identifier to “link” the tables. The reason to use these types of ids instead of the primary MicrobeDB ids is that the NCBI ids will remain the same between MicrobeDB versions. Use the following fields:
  • To extend a Genomeproject, use the field “gp_id”
  • To extend a Replicon, use the field “rep_accnum”
  • To extend a Gene, use the field “gid” or “pid”
• For example, imagine you wanted to store SNP data. You want to store the position of the SNP, an in-house experiment id, and the base at that position. Then you would want to create a new table and use the rep_accnum field to join the MicrobeDB replicon table to your in-house table. Your columns would be “your_primary_snp_id”, “rep_accnum”, “your_experiment_id”, “snp_position”, “snp_base”.