Difference between revisions of "Ajvree Week 13"

Latest revision as of 18:56, 21 November 2013

[edit] 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

[edit] 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

[edit] 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:

Table Analysis

• looked at tables within E3 gdb file to find inconsistencies in data

Systems Table

• There are missing dates for quite a few gene ID systems

OrderedLocusNames Table

• All ID's took the expected form, SP_####

UniProt Table

• ID's are scattered. Have a general pattern of beginning with P or Q, following with five characters (mix of numbers and letters)

RefSeq Table

• all ID's in form NP_######

[edit] Links

Streptococcus pneumoniae

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

Data Information

• Kmeilak Week 10, Kmeilak Week 11, Kmeilak Week 12, Kmeilak Week 13
• Taur.vil Week 10, Taur.vil Week 11, Taur.vil Week 12, Taur.vil Week 13, Taur.vil Week 14, Taur.vil Week 15
• Ajvree Week 10, Ajvree Week 11, Ajvree Week 12, Ajvree Week 13, Ajvree Week 14, Ajvree Week 15