Fix for import_mothur cutoff and missing taxa #412
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When using import_mothur provided cutoff values were ignored due to missing return(cutoff) argument. When using import_mothur provided cutoff values were ignored due to missing return(cutoff) argument. Additionally the last two OTUs were missing because as.integer(rawlines[2]) gives back the number of OTUs but rawlines contains two more elements (cutoff and number of OTUs). Additionally the last two OTUs were missing because as.integer(rawlines[2]) gives back the number of OTUs but rawlines contains tow more elements (cutoff and number of OTUs).
mothur fn.list file now contains a label row. When not providing a cutoff value this leads to an error.
…tion In the mothur_constaxonomy_file the OTUs are named: Otu01, Otu02, etc., because phyloseq uses a different naming system you get a "Component taxa/OTU names do not match." error message. I have created a new function called "create_otu_dict" which is used to name the OTUs of the mothur_constaxonomy_file the same way as phyloseq does. Additionally I added a new option for parsing the elements of a taxonomy vector called "parse_taxonomy_mothur". mothur taxonomy files in general have the following six ranks: Kingdom, Phylum, Class, Order, Family, Genus).
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When using import_mothur provided cutoff values were ignored due to
missing return(cutoff) argument.
Additionally the last two OTUs were missing because
as.integer(rawlines[2]) gives back the number of OTUs but rawlines
contains two more elements (cutoff and number of OTUs).