Difference between revisions of "Phenote .ace citace upload"

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Line 51: Line 51:
 
#Number '''life stage objects'''
 
#Number '''life stage objects'''
 
#Number '''anatomy terms'''
 
#Number '''anatomy terms'''
#Number '''alleles linked to phenotype terms:'''   
+
#Number '''alleles-phenotype links:'''   
 
  use either AQL query
 
  use either AQL query
 
  select all class variation where exists_tag ->phenotype
 
  select all class variation where exists_tag ->phenotype

Revision as of 18:08, 4 April 2008

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Dumping Phenote into .ace file

Connect to tazendra

: ssh  acedb@tazendra.caltech.edu
Pswd
: cd /home/acedb/work/allele_phenotype
: ls //will see previous .ace files ‘allele_phenotype.ace.<date> and err.out.<date> along with dump script -  use_package.pl* ->  .ace file program//  run script
: ./use_package.pl  //dump info into .ace file command//

New allele_phenotype.ace and err.out files will be created as noted by date at the end of each. Send them to Allele_Phene_Dump on scoobydoo:

: scp err.out.2008XX yook@scoobydoo.caltech.edu:/Users/Yook/WS_latest/ace_phenote_dump  
: scp allele_phenotype.ace.2008XX yook@scoobydoo.caltech.edu:/Users/Yook/WS_latest/ace_phenote_dump 

Open err.out to see if any errors were generated during the dump process.

Errors in .ace file generated form should be indicated by "ERROR" in the .ace output, or as comments at the top of the form.

<left over from CGI .ace dump instructions> Is this still necessary? Make sure that there are no obsolete phenotype annotations: - Script for finding obsolete terms is find_obsolete.pl at path listed below on tazendra: /home/Postgres/work/citace_upload/allele_phenotype/

NOTE: Over time these dump files will add up, so please clean it up from time to time.

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 on spica

Send new allele_phenotype.ace to kyook on spica:

: scp <.ace dump files> kyook@spica.caltech.edu:/home3/kyook/alle_phen.ace.latest

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 /Users/Yook/WS_latest/WS188

Comparing data builds: From the latest build, record

  1. Number strain objects
  2. Number life stage objects
  3. Number anatomy terms
  4. Number alleles-phenotype links:
use either AQL query
select all class variation where exists_tag ->phenotype
select a, a-> variation from a in class phenotype where exists_tag a ->variation

Number variations that are alleles: use WQL

find variation variation_type=allele

or AQL

select g from g in class variation where exists_tag g-> allele 

Checking that the .ace dump file is readable: Load in .ace dump Hit ‘Edit..‘ button Choose ‘Read .ace file’ Accept change in write priviledges 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.

Checking that the file does not alter any objects it shouldn’t: Once .ace dump loaded in 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 XXXXX citace@altair:~/Data_for_citace/Data_from_<YOU> /home/citace/Data_for_citace/Data_from_<YOU>/ <allele_phenotype_dump_WSxxx.ace>