Updating ontology (.obo) files for the OA
Contents
Updating local acedb to latest available WS (instructions from Wen)
You have to download the latest build from the Sanger website. From the command line (X11 on Mac OS), go to the local directory where the old WS is installed. Login anonymously to Sanger’s ftp site
bash-3.2$ ftp ftp.sanger.ac.uk Connected to ftpservice2.sanger.ac.uk. 220-ftp.sanger.ac.uk NcFTPd Server (free educational license) ready. 220-Wellcome Trust Sanger Institute FTP server 220- 220-Problems after login? Try using '-' as the first character of you 220-password. 220- 220-**** 220-**** 220-**** 7/9/06 FTP Server upgraded please report any problems to 220-**** ftpadmin@sanger.ac.uk 220-**** 220 Name (ftp.sanger.ac.uk:Yook): anonymous 331 Guest login ok, send your complete e-mail address as password. Password:
Go to directory containing WS releases Download whole release (takes about 1 hour) Quit ftp
FTP> cd pub/wormbase FTP> get WS188.tar [or get –R WS188 for Ncfp client] FTP> bye
Unzip tar Get into the new WS directory and run install to install new database (~15 minutes)
$ tar –xvvf WS188.tar $ cd WS188 $./INSTALL
The readout after installation is as follows:
ACEDB installation script:
Yook will be known as the acedb-administrator
We are going to install the acedb system in the present directory:
/Users/Yook/WS_latest/WS188
This is your available disk space in this directory:
Filesystem 1024-blocks Used Available Capacity Mounted on
/dev/disk0s2 488050672 149925748 337868924 31% /
The amount of space you need will depend on what data you are installing.
For the source code and binary, you need around 15 Mb.
Should we proceed? Please answer yes/no : yes
Exchange newest release with older one by removing old release and or change ./xace launch path to new release etc. $ rm <old WS release>
Updating .obo files
Retrieving object connections from the latest build files
Variation-gene and variation-paper connection information retrieved in phenote depends on information from the latest WS. After the upload, these .obo files in Postgres need to be repopulated with the most current information.
Run queries on the latest WS release for the most current information (it probably matters that the queries maintain the same column output?)
Allele_gene connections
To: Find all variations in the allele group (excludes SNPs etc.) along with the WBGeneID and public gene name of the gene they are assigned, if that is available.
Run the following AQL: select a, a->gene, a->gene->public_name from a in class variation where exists_tag a->allele
- Sort results (optional)
- Export as WS#_vargene into /Users/Yook/Postgres on scoobydoo (choose Separator character set to blank (TAB))
- As of WS189 this query returns 20653 lines, and includes all alleles and in some cases, multiple genes linked to an allele (e.g.isoforms, alt gene models etc.)
Transgene_summary_paper connections
To: List transgenes already linked to a paper
Run the following AQL: select t, t->reference, t->summary from t in class transgene where exists t->reference
- Sort results (optional)
- Export as WS#_transpapsum into /Users/Yook/Postgres on scoobydoo (choose Separator character set to blank (TAB))
- As of WS189 this query returns 5473 lines
Rearrangement_inside_gene connections
To: List rearrangements with LG, 'genes inside' and ‘gene outside’ (public names only)
Run the following AQL: select r, r->map, r->gene_inside->public_name, r->gene_outside->public_name from r in class rearrangement
- Sort results (optional)
- Export as WS#_rearragene into /Users/Yook/Postgres on scoobydoo (choose Separator character set to blank (TAB))
- As of WS189 this query returns 10054 lines
Repopulating Postgres
Two scripts need to be run to populate Postgres with the updated variation information. It is important to run these scripts every time the variation information is updated. The scripts are on tazendra and run off of files Variation_gene.txt, transgene_summary_reference.txt and rearr_simple.txt. So files need to be transferred to tazendra and renamed to be recognizable by those scripts.
Transfer files to tazendra
Scripts are stored in acedb@tazendra.caltech.edu:/home/acedb/karen/populate_gin_variation
Rename WS189_vargene.txt to Variation_gene.txt
$scp WS189_vargene.txt acedb@tazendra.caltech.edu:/home/acedb/karen/populate_gin_variation/Variation_gene.txt
Rename WS189_rearragene.txt to rearr_simple.txt
$scp WS189_rearragene.txt acedb@tazendra.caltech.edu:/home/acedb/karen/populate_gin_variation/rear_simple.txt
Rename WS189_transpapsum to transgene_summary_reference.txt
$scp WS189_transpapsum.txt acedb@tazendra.caltech.edu:/home/acedb/karen/populate_gin_variation/transgene_summary_reference.txt
Scripts to populate Phenote .obo files
- populate_ali_alleleinfo.pl updates information based on Variation_gene.txt and transgene_summary_reference.txt. Make sure files are named accordingly or the program won’t see them.
- make_obo.pl creates a text .obo based on rearr_simple.txt and Variation_gene.txt. This script populates the WS current info.
Both apps are on tazendra in the same directory as the updated variation info.
cd to /home/acedb/karen/populate_gin_variation/ $ ./populate_ali_alleleinfo.pl $ ./ make_obo.pl
NOTE: populate_gin_variation updates data based on variation_tab_wbgene file (in postgres / cgi) , which is no longer current.
To check if the re-population scripts worked, check out the WS_current info field The date will tell you when it was last updated; it should reflect the date the script was run.
--kjy
