Difference between revisions of "Ksherbina Week 9"

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(Lab Notebook: Added another command that was run using XMLPipeDB match)
(Lab Notebook: Added sql query)
Line 40: Line 40:
 
  java -jar xmlpipedb-match-1.1.1.jar "VC_(A|)[0-9][0-9][0-9][0-9]" < UniProt_V_cholerae_KSTV_20131022
 
  java -jar xmlpipedb-match-1.1.1.jar "VC_(A|)[0-9][0-9][0-9][0-9]" < UniProt_V_cholerae_KSTV_20131022
 
3831 unique matches were found.
 
3831 unique matches were found.
 +
*Count the number of unique gene IDs using an SQL query:
 +
select count(*) from genenametype where type = 'ordered locus' and value ~ 'VC_(A|)[0-9][0-9][0-9][0-9]'
 +
Count = 3831

Revision as of 17:15, 24 October 2013

Katrina Sherbina
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Export Information

Version of GenMAPP Builder: 2.0b70

Computer on which export was run: Personal computer

Postgres Database name: VC_KS_20131022_gmb2b70

UniProt XML filename: UniProt_V_cholerae_KSTV_20131022.xml

  • UniProt XML version (The version information can be found at the UniProt News Page): UniProt release 2013_10
  • Time taken to import: 4.20 minutes

GO OBO-XML filename: go_daily-termdb_KS_20131022.obo-xml

  • GO OBO-XML version (The version information can be found in the file properties after the file downloaded from the GO Download page has been unzipped):
  • Time taken to import: 8.81 minutes
  • Time taken to process: 7.33 minutes

GOA filename: 46.V_cholerae_ATCC_39315_KS_20131022.goa

  • GOA version (News on this page records past releases; current information can be found in the Last modified field on the FTP site):
  • Time taken to import: 0.10 minutes

Name of .gdb file: Vc-Std_KS_20131022.gdb

  • Time taken to export .gdb:
  • Start Time: 6:50 pm
  • End Time: 9:22 pm

Note:

Lab Notebook

  • Use XMLPipeDB Match to count the number of unique gene ideas in the V. cholerae Uniprot XML file.
java -jar xmlpipedb-match-1.1.1.jar "VC_[0-9][0-9][0-9][0-9]" < UniProt_V_cholerae_KSTV_20131022

2738 unique matches were found.

java -jar xmlpipedb-match-1.1.1.jar "VC_(A|)[0-9][0-9][0-9][0-9]" < UniProt_V_cholerae_KSTV_20131022

3831 unique matches were found.

  • Count the number of unique gene IDs using an SQL query:
select count(*) from genenametype where type = 'ordered locus' and value ~ 'VC_(A|)[0-9][0-9][0-9][0-9]'

Count = 3831

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