Difference between revisions of "Updating ontology (.obo) files for the OA"
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Transfer files to acedb@tazendra.caltech.edu:/home/acedb/karen/populate_gin_variation | Transfer files to acedb@tazendra.caltech.edu:/home/acedb/karen/populate_gin_variation | ||
− | + | Rename '''WS188_vargene.txt''' to '''''Variation_gene.txt''''' | |
$scp WS188_vargene.txt acedb@tazendra.caltech.edu:/home/acedb/karen/populate_gin_variation/Variation_gene.txt | $scp WS188_vargene.txt acedb@tazendra.caltech.edu:/home/acedb/karen/populate_gin_variation/Variation_gene.txt | ||
− | Rename WS188_rearragene.txt to | + | Rename '''WS188_rearragene.txt''' to '''''rearr_simple.txt''''' |
$scp WS188_rearragene.txt acedb@tazendra.caltech.edu:/home/acedb/karen/populate_gin_variation/rear_simple.txt | $scp WS188_rearragene.txt acedb@tazendra.caltech.edu:/home/acedb/karen/populate_gin_variation/rear_simple.txt | ||
− | Rename WS188_transpapsum to transgene_summary_reference.txt | + | Rename '''WS188_transpapsum''' to '''''transgene_summary_reference.txt''''' |
$scp WS188_transpapsum.txt acedb@tazendra.caltech.edu:/home/acedb/karen/populate_gin_variation/transgene_summary_reference.txt | $scp WS188_transpapsum.txt acedb@tazendra.caltech.edu:/home/acedb/karen/populate_gin_variation/transgene_summary_reference.txt | ||
− | + | Runscripts to populate Phenote .obo files | |
− | There are two scripts, populate_ali_alleleinfo.pl and make_obo.pl that 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. | + | There are two scripts, '''''populate_ali_alleleinfo.pl''''' and '''''make_obo.pl''''' that 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. |
Both apps are on tazendra in the same directory as the updated variation info. | Both apps are on tazendra in the same directory as the updated variation info. | ||
− | Run scripts: | + | :Run scripts: |
− | cd to /home/acedb/karen/populate_gin_variation/ | + | cd to /home/acedb/karen/populate_gin_variation/ |
− | $ ./populate_ali_alleleinfo.pl | + | $ ./populate_ali_alleleinfo.pl |
− | $ ./ make_obo.pl | + | $ ./ make_obo.pl |
− | populate_ali_alleleinfo.pl updates information based on Variation_gene.txt and | + | '''''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. | 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 | + | '''''make_obo.pl''''' creates a text .obo based on rearr_simple.txt and |
Variation_gene.txt. This script populates the WS current info. | Variation_gene.txt. This script populates the WS current info. | ||
Line 62: | Line 62: | ||
file (in postgres / cgi) , which is no longer current. | file (in postgres / cgi) , which is no longer current. | ||
− | To check if the repopulation scripts worked, check out the | + | To check if the repopulation scripts worked, check out the [http://tazendra.caltech.edu/~azurebrd/var/work/phenote/ws_current.obo WS_current] info field |
− | http://tazendra.caltech.edu/~azurebrd/var/work/phenote/ws_current.obo | ||
The date will tell you when it was last updated; it should reflect the date the script was run. | The date will tell you when it was last updated; it should reflect the date the script was run. | ||
Revision as of 23:11, 13 March 2008
Contents
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 ->WS#_vargene -> Variation_gene.txt
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 g, g->gene, g->gene->public_name from g in class variation where exists_tag g-> allele
- Sort results (optional)
- Export as WS#_vargene into folder Phenote on local desktop (choose Separator character set to blank (TAB))
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 folder Phenote on Desktop (choose Separator character set to blank (TAB))
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 folder Phenote on Desktop (choose Separator character set to blank (TAB))
Repopulating Postgres
Transfer files to acedb@tazendra.caltech.edu:/home/acedb/karen/populate_gin_variation
Rename WS188_vargene.txt to Variation_gene.txt
$scp WS188_vargene.txt acedb@tazendra.caltech.edu:/home/acedb/karen/populate_gin_variation/Variation_gene.txt
Rename WS188_rearragene.txt to rearr_simple.txt
$scp WS188_rearragene.txt acedb@tazendra.caltech.edu:/home/acedb/karen/populate_gin_variation/rear_simple.txt
Rename WS188_transpapsum to transgene_summary_reference.txt
$scp WS188_transpapsum.txt acedb@tazendra.caltech.edu:/home/acedb/karen/populate_gin_variation/transgene_summary_reference.txt
Runscripts to populate Phenote .obo files There are two scripts, populate_ali_alleleinfo.pl and make_obo.pl that 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. Both apps are on tazendra in the same directory as the updated variation info.
- Run scripts:
cd to /home/acedb/karen/populate_gin_variation/ $ ./populate_ali_alleleinfo.pl $ ./ make_obo.pl
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.
NOTE: populate_gin_variation updates data based on variation_tab_wbgene file (in postgres / cgi) , which is no longer current.
To check if the repopulation 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