Difference between revisions of "Blitvak Week 14"

Revision as of 03:58, 5 December 2015

12/1

• Goals: Consult with Anu to make modifications to TallyEngine/GenMAPP (share initial export results)
• Reacquaint with using Excel to track IDs/discrepant IDs (Using Microsoft Excel to Compare ID Lists)
• pgAdmin III work will be involved, in conjunction with Excel, for the new modified .gdb: Will use: select value from genenametype where type = 'ordered locus'; and will export (and use with Excel)

B.cenocepacia_J2315_20151201_gmbuilder-genialomics-20151201

ORF not ORDEREDLOCUS

• XML - 3.72 minutes
• OBO/XML - 5.25 minutes
  • Processing: 3.91 minutes
• GOA - 0.04 minutes

EXPORT START: 10:27 PM

END: 2:49 AM

12/3

'p?BCA[A-Z]?[0-9][0-9][0-9][A-Z]?[0-9]?[A-Z, a-z]?';

select count(*) from genenametype where type = 'ordered locus' and value ~ 'p?BCA[M,S,L][0-9][0-9][0-9][A,a]?[0-9]?[A-Z, a-z]?';

MODIFIED: 'p?BCA[M,S,L]?[0-9][0-9][0-9][A,a]?[0-9]?[A-Z, a-z]?';

first object xml editor

6 IDs with problems

bca199f

select count(*) from genenametype where type = 'ORF' and value ~ 'p?BCA[L,M,S]?[0-9][0-9][0-9][A,a]?[0-9]?[A-Z, a-z]?';

• BUILD 3
• XML - 3.99 minutes
• OBO/XML- 5.77 minutes (1), 4.06 minutes (2)
• GOA - 0.05 minutes

START: 7:24 p END: 12:01 a

• BUILD 4
• XML - 3.46 minutes
• OBO/XML - 5.05 minutes, 3.75 minutes (2)
• GOA - 0.04 minutes

START: 7:51 a END: 6:57 p

'[pBCA,BCAL,BCAS,BCAM][0-9][0-9][0-9][A,a]?[0-9]?[A-Z, a-z]?'; '(pBCA)?(BCAL)?(BCAS)?(BCAM)?[0-9][0-9][0-9][A,a]?[0-9]?[A-Z, a-z]?';