Ajvree Week 13
From LMU BioDB 2013
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
| Alina's User Page | Kevin's User Page | Tauras's User Page |
| Biological Databases Class Page | Gene Database Project | Gene Database Project Report Guidelines |
- Import Export Cycle 1: tATK Export One: TIGR4 Testing Report
- Import Export Cycle 2: tATK E2: TIGR4 Testing Report
- Import Export Cycle 3: tATK E3: TIGR4 Testing Report
- Import Export Cycle 4: tATK E4: TIGR4 Testing Report
| Project Roles: | Project Manager | Coder | GenMAPP User | Quality Assurance |
