Blitvak Week 15

12/8

7121 - orf

6993 - uniprot

128 - diff

205 - query for duplicates

77 - number of records

128 + 77 = 205

java -jar xmlpipedb-match-1.1.1.jar "p?BCA[L,S,M]?[0-9][0-9][0-9][A,a]?[0-9]?[A-Z, a-z]?" < "uniprot-taxonomy%3A216591_GEN_BL12_20151119.xml"

• select genetype_name_hjid, count(value) from genenametype where type = 'ORF' and value ~ 'p?BCA[LMS]?[0-9][0-9][0-9][Aa]?[0-9]?[A-Z,a-z]?' group by genetype_name_hjid;

• select genetype_name_hjid, count(value) from genenametype where type = 'ORF' and value ~ 'p?BCA[LMS]?[0-9][0-9][0-9][Aa]?[0-9]?[A-Z,a-z]?' group by genetype_name_hjid having count(value) > 1;

• select sum(dupe_count) from (select genetype_name_hjid, count(value) as dupe_count

   from genenametype where type = 'ORF' and value ~ 'p?BCA[LMS]?[0-9][0-9][0-9][Aa]?[0-9]?[A-Z,a-z]?'
   group by genetype_name_hjid having count(value) > 1 order by count(value) desc) as dupe_tally;

• select genetype_name_hjid, count(value) as dupe_count

   from genenametype where type = 'ORF' and value ~ 'p?BCA[LMS]?[0-9][0-9][0-9][Aa]?[0-9]?[A-Z,a-z]?'
   group by genetype_name_hjid having count(value) > 1 order by count(value) desc;

• select *

   from genenametype where genetype_name_hjid = 66138;

• select genetype_name_hjid, count(value) from genenametype where type = 'ORF' and value ~ 'p?BCA[LMS]?[0-9][0-9][0-9][Aa]?[0-9]?[A-Z,a-z]?' group by genetype_name_hjid having count(value) > 1 order by count(value) desc;

For Presentation

Final command for MATCH:

• java -jar xmlpipedb-match-1.1.1.jar "p?BCA[L,S,M]?[0-9][0-9][0-9][A,a]?[0-9]?[A-Z, a-z]?" < "uniprot-taxonomy%3A216591_GEN_BL12_20151119.xml"
• select count(*) from genenametype where type = 'ORF' and value ~ 'p?BCA[L,S,M]?[0-9][0-9][0-9][A,a]?[0-9]?[A-Z, a-z]?';