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leffj / mctoolsr

Microbial community analysis tools in R
http://leffj.github.io/mctoolsr/
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.biom vs .txt loading w/euk SILVA classifications #17

Closed amoliverio closed 8 years ago

amoliverio commented 8 years ago

loading taxa table + mapping file as input works with .biom output but not .txt output for taxonomy from SILVA

error message with text file (and works fine with same file in biom format):

116 samples loaded Warning message: In .parse_taxonomy(data$taxonomy) : Issue with provided taxonomy. Check for quotes near line 2. Proceeding without taxonomy.Issue with provided taxonomy. Check for quotes near line 9. [... truncated]

leffj commented 8 years ago

Thanks for letting me know. Would you mind attaching a reduced mapping file/otu table that is having the problem so I can troubleshoot?

amoliverio commented 8 years ago

for mctoolsr.zip

leffj commented 8 years ago

Fixed in v0.0.1.1. Note that the issue was caused by each taxon having many (>15) taxonomy levels, which could be problematic for other reasons, so it's probably better to used the reduced SILVA taxonomy with fewer levels.