Ajvree Week 13

Week 12 Information

Export Counting: -open Access, open file (remember to change all to all files) TIGR4 file:
ids used: SP_####
orderedlocusnames count total: 2126 entries
R6 file:
orderedlocusnames count total: 2115 entries
ids used: SPG_####
G54 file:
ids used: SPG_####
orderedlocusnames count total: 2115 entries
After finding identical results for R6 and G54 files, realized that R6 file was actually for the G54 strain. Checked a few times (reopened files multiple times to confirm)
First try on Tally Engine for TIGR4:
XML Count:
orderedlocus: 2127
refseq: 2106
Database Count:
ordered locus: 3831
refseq: 3403

Week 13

Tally Engine:

created new database in pgadmin III
in sql, opened gmbuilder.sql
ran query, database tables were inserted
went in to tally engine and imported files
- Xml import took 5.41 min
- GOA import took 0.07 min
unzipped go-xml file
OBO-XML import time: 19.92 min
additional gene ontology information was processed, this took 14.96 min
ran tally, came up with error
refreshed gmbuilder and tried again successfully

Results:

XMLpipedb Match

downloaded program from sourceforge
opened cmd program
cd Downloads file
moved xmlmatch jar file to download folder
used match to look for pattern SP_[0-9][0-9][0-9][0-9]
Total unique matches: 2126
almost identical to tally engine results of 2127, minus one result

Results:

OriginalRowCounts

Looked at TIGR4 gdb file and benchmard VD file for table similarities/differences
seemed to have same tables/same information
took screenshots of both, included here:

TIGR4: Benchmark:

Note: a few of the rows are missing in the benchmark screenshot- could not fit all of them on screen.

SQL

used following query to search for matches:
- select count(*) from genenametype where type = 'ordered locus' and value ~ 'SP_[0-9][0-9][0-9][0-9]';
Result given was 2126

11/21/13

Tally Engine for Export 3

downloaded Taurus's version of gmbuilder to redo tally engine counting
used export 3 files instead of previous export 1 files
connected to avreelan database in pgadminIII, inserted new gmbuilder tables
opened new version of gmbuilder/tally engine, connected to avreelan database
XML file import took: 2.02 min
OBO-XML file import took: 6.25 min
- additional gene ontology data processing took: 4.81 min
GOA file import took: 0.04 min
Results:
- GeneId's now visible, total of 2105 in both xml and database counts
- orderedlocusnames still at same value of 2126 in both xml and database counts
- screenshot:

Original Row Counts for Export 3

redid row counts using the export 3 file
compared with benchmark file
both files had identical number of tables with same categories in each, although some were out of order.
Screenshots:

E3 TIGR4: Benchmark: