Package 

Class CountNsInRawHapSequencesPlugin

  • All Implemented Interfaces:
    java.lang.Runnable , net.maizegenetics.plugindef.Plugin , net.maizegenetics.plugindef.PluginListener , net.maizegenetics.util.ProgressListener 
    @Deprecated() 
public class CountNsInRawHapSequencesPlugin
extends AbstractPlugin

    NOTE: THis test is obsolete - uses old schema and old connection method. Calculates the percentage of N's for each "raw" haplotype (ie, not consensus) for each genome interval (anchor, not inter-anchors). Results shoudl be printed to a tab-delimited file with genome_interval_id as rows, and taxa/percentage as the columns. Testing: Testing was done by random manual checking. Once the output file is created, it is uploaded to excel. use sqlite3 on machine holding db. Look at sequences and verify when it has "1" as percent, there are all N's. WHen 0, there are 0. When a percentage, e.g. .53, the sequence looks to be half N's. Find gamete_grp_id for the line you want to check: sqlite> SELECT gamete_haplotypes.gamete_grp_id FROM gamete_haplotypes sqlite> INNER JOIN gametes ON gametes.gameteid=gamete_haplotypes.gameteid sqlite> INNER JOIN genotypes on gametes.genoid=genotypes.genoid sqlite> WHERE genotypes.line_name='CML247'; sqlite> 5 (this is returned value) Then look at the sequence: sqlite> select gamete_grp_id, genome_interval_id,sequence from haplotypes where gamete_grp_id=5 and genome_interval_id=111;