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Remove reftaxonomy parameters or fix daughter level bug #241

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mothur-westcott opened this Issue May 23, 2016 · 1 comment

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Bugs Command:Classify.otu Command:Summary.tax
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  Version 1.38.0
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mothur-westcott commented May 23, 2016

Causes bug with new addition of parent taxonomy

Warning: cannot find taxon Turicibacter_unclassified in reference taxonomy tree at level 6 for GQY1XT001BIPNI. This may cause totals of daughter levels not to add up in summary file.
Warning: cannot find taxon Turicibacter_unclassified in reference taxonomy tree at level 6 for GQY1XT001CS85M. This may cause totals of daughter levels not to add up in summary file.

@mothur-westcott mothur-westcott added Bugs Command:Classify.otu Command:Summary.tax labels May 23, 2016

@mothur-westcott mothur-westcott added this to the Version 1.38.0 milestone May 23, 2016

@mothur-westcott mothur-westcott added a commit that referenced this issue Jun 30, 2016

@mothur-westcott mothur-westcott Removes reftaxonomy from summary.tax 
#241
 b598f39

@mothur-westcott mothur-westcott added a commit that referenced this issue Jun 30, 2016

@mothur-westcott mothur-westcott Modifies picrust option to accept new unclassified format 
Parent_unclassified

#241
 e41f158
@mothur-westcott
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mothur-westcott commented Jun 30, 2016

Removed reftaxonomy parameter from classify.otu and summary.tax.
Modified make.biom picrust functions to handle parent_unclassified taxons in gg searches.

Completed with commit b537dde

@mothur-westcott mothur-westcott closed this Jun 30, 2016

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