mlangill / microbedb Goto Github PK

Datatypes for gene.protein_accnum and replicon.rep_accnum should be changed from char(12) to a longer datatype. Currently data is being truncated. I'd recommend varchar(50).

Data dump of MicrobeDB schema is missing auto-increment for primary indexes. Need to change mysqldump options to fix this.

I've just downloaded and am trying to use the software, however i'm getting errors in the initial testing phase.

Log of attempt:
2016/01/26 14:21:13> Downloading file: Bacteria_2016-01-26/NCBI_orginfo.txt from Dropbox at: http://dl.dropbox.com/u/5329340/NCBI_orginfo.txt
2016/01/26 14:21:14> Problem with downloading! Waiting 60 seconds before attempting again.
2016/01/26 14:21:22> Error with downloading the new version: No such file or directory

I checked the url: http://dl.dropbox.com/u/5329340/NCBI_orginfo.txt and it gave a delightful 404 error.

scripts/download_version.pl: line 327:
#Note4: As of Nov. 15,2012 the metadata files are not available from NCBI ftp site. As temporary solution I have obtained the most recent metadata as of June 2012 and I am hosting these files via Dropbox. Therefore, metadata will only exist for genomes deposited before this date.

Is there something this can be replaced with? It clearly is not for recent genomes, as only the ones before 06/2012 are available.

In Note3 the file ftp://ftp.ncbi.nlm.nih.gov/genomes/GENOME_REPORTS/prokaryotes.txt is mentioned as still using older genome ids, not the latest BioProject ids. Is this still the case?

Thanks for your help!
-Benjamin-

Any update to the dropbox link and the NCBI folder paths in the works?

Here is an example of multiple messages of error like the one below.
Is there a solutions?
Thank you

2014/12/09 10:30:55> Working on /repos/MicrobeDB/share/Bacteria_2014-12-08/Arthrobacter_chlorophenolicus_A6_uid58969/
/repos/MicrobeDB/share/Bacteria_2014-12-08/Arthrobacter_chlorophenolicus_A6_uid58969/NC_011879.gbk
/repos/MicrobeDB/share/Bacteria_2014-12-08/Arthrobacter_chlorophenolicus_A6_uid58969/NC_011881.gbk
/repos/MicrobeDB/share/Bacteria_2014-12-08/Arthrobacter_chlorophenolicus_A6_uid58969/NC_011886.gbk2014/12/09 10:30:55> Parsing file: /repos/MicrobeDB/share/Bacteria_2014-12-08/Arthrobacter_chlorophenolicus_A6_uid58969/NC_011879.gbk
2014/12/09 10:30:56> Couldn't add the following to microbedb: /repos/MicrobeDB/share/Bacteria_2014-12-08/Arthrobacter_chlorophenolicus_A6_uid58969/ ! Reason:
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: start [426645] is greater than end [617].
If you want to truncated and reverse complement,
you must call trunc followed by revcom. Sorry.
STACK: Error::throw
STACK: Bio::Root::Root::throw /Library/Perl/5.18/Bio/Root/Root.pm:449
STACK: Bio::PrimarySeqI::trunc /Library/Perl/5.18/Bio/PrimarySeqI.pm:456
STACK: Bio::SeqFeature::Generic::seq /Library/Perl/5.18/Bio/SeqFeature/Generic.pm:705
STACK: MicrobeDB::Parse::parse_gbk ../../MicrobeDB/Parse.pm:232
STACK: MicrobeDB::Parse::parse_genome ../../MicrobeDB/Parse.pm:94
STACK: main::load_microbedb /Users/frederic.foucault/repos/MicrobeDB/scripts/load_version.pl:119
STACK: /Users/frederic.foucault/repos/MicrobeDB/scripts/load_version.pl:95

This confused someone in the lab (including me)

Thanks for the software

End users will likely want to add their own fields to the tables in MySQL. For example, users may want to have another field for additional annotations for genes. Currently the MicrobeDB API breaks if a user tries to access a new mysql field since the field names are hard coded in each of Class modules (GenomeProject.pm, Replicon.pm, etc).

Most obvious solution is to move the column names into a config file that could be update by the user.

A more elegant solution would be to obtain the column names from the database first before searching.