Phenote .ace citace upload
Contents
Dumping phenotype app_files into .ace
Two dumping scripts are required to capture all of the allele phenotype data, both on tazendra:
/home/acedb/karen/WS_upload_scripts/phenotype/use_package.pl*
/home/acedb/karen/WS_upload_scripts/paper_object/get_paper_object.pl*
allele_phenotype and paper_object are dumped on a weekly cron job Sundays at 4am
see /home/acedb/cron/crontab_20140703
0 4 * * sun /home/acedb/karen/WS_upload_scripts/paper_object/get_paper_object.pl 0 4 * * sun cd /home/acedb/karen/WS_upload_scripts/transgene; ./use_package.pl 0 4 * * sun cd /home/acedb/work/allele_phenotype/; ./use_package.pl
/home/acedb/karen/WS_upload_scripts/phenotype/use_package.pl :
This script creates 5 files:
- allele_phenotype.ace.<timestamp>
- var_phen.ace
- mol_phene.ace.<timestamp>
- mol_phene.ace
- err.out.<timestamp>
var_phen.ace and mol_phen.ace are copies of allele_phenotype.ace and mol_phene.ace.
var_phen.ace and mol_phen.ace are picked up by spica on a cron job that is run every Monday at 8am.
/home/acedb/karen/WS_upload_scripts/paper_object/get_paper_object.pl*:
This script creates a file that will associate phenotype annotated alleles with their respective genes.
This is needed so references from phenotype annotations are added to the references on the respective gene page.
And example from this file:
Paper : WBPaper00000005 Gene WBGene00000898 Allele "WBVar00143949" Inferred_Automatically "Inferred automatically from curated phenotype" Gene WBGene00004015 Allele "WBVar00000103" Inferred_Automatically "Inferred automatically from curated phenotype" Gene WBGene00004015 Allele "WBVar00000103" Inferred_Automatically "Inferred automatically from curated phenotype"
Dumping allele_paper connections into .ace file
is at :
/home/acedb/..../get_paper_object.pl
Run it by going to that directory and redirecting output to a file
./get_paper_object.pl > file
If there are errors, which is rare, they will look something like:
// ERR There's an object that has no name and no type, but still has a paper. It has postgres database ID 2712 testdb=> SELECT * FROM app_tempname WHERE joinkey = '2712'; joinkey | app_tempname |app_timestamp ---- +--------------+--------------- ... ---- +------------------+--------------- ... ---- +-----------------+------------------------------- 2712 | WBPaper00002087 | 2006-07-11 11:52:20.208295-07 (1 row) Here's all the data for it when it got migrated from the CGI
Testing Phenote .ace for upload
Evaluate how the uploaded data impacts WB by comparing object numbers before and after data upload. This means that you need access to the latest WS and have the means to edit the WS to read the .ace dump.
Test file locally on Acedb
This step is to test two things: First, that the file is readable. Second, that the file does not alter any objects it shouldn’t.
Launch local acedb:
$ cd Desktop/acedb $ ./xace /.../WSXXX/acedb
Comparing data builds: From the latest build, record
- Number strain objects
- Number life stage objects
- Number anatomy terms
- Number variation'-phenotype connection'
use either AQL query:
select all class variation where exists_tag ->phenotype select p, p-> variation from p in class phenotype where exists_tag p->variation
- 5. Number variations that are alleles:
use WQL
find variation variation_type=allele
or AQL
select a from a in class variation where exists_tag a->allele
- 6. Number alleles with a phenotype
Find all alleles with a phenotype
select v from v in class variation where exists_tag v->phenotype
Check that the .ace dump file is readable:
to load in .ace dump
Select ‘Edit..‘ ‘Read .ace file’, Accept change in write privileges, Select ‘Open ace file’, Find and select file to open, Select ‘Read all’
If the .ace file is okay, then 100% of the lines will have been read in. This will be noted in the second line called ‘Line:’. If the dump produced a bad file, the read in will stop at the point where the problem occurred. You can go to that line in the .ace file and check it out.
Check that the file does not alter any objects it shouldn’t:
Once .ace dump is loaded in to acedb, redo counts for all objects as above. Compare object numbers between latest database and new .ace file to make sure data in the dump looks reasonable, i.e., no lost data or inflated numbers.
Uploading .ace for Wen into Citace
Deposit .ace for Wen in citace:
scp var_phen.ace xxxx@xxxx.caltech.edu:/.../Data
