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12
egrace479 commited on
Commit
c028254
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1 Parent(s): 0436b05

Add output of check_taxa script for original dataset and this update.

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  1. data/missing_taxa_output.txt +44 -0
data/missing_taxa_output.txt ADDED
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+ Output of Data Check for First Full Version of BioCLIP training data (initial submission):
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+ [2023-10-25 10:20:12,498] [WARNING] [root] There are 5 kingdoms instead of 3.
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+ [2023-10-25 10:20:13,673] [WARNING] [root] 1300744 entries are missing rank kingdom, but have genus label.
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+ [2023-10-25 10:20:13,918] [WARNING] [root] 1302578 entries are missing rank phylum, but have genus label.
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+ [2023-10-25 10:20:14,168] [WARNING] [root] 2368981 entries are missing rank class, but have genus label.
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+ [2023-10-25 10:20:14,402] [WARNING] [root] 1344781 entries are missing rank order, but have genus label.
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+ [2023-10-25 10:20:14,637] [WARNING] [root] 1310177 entries are missing rank family, but have genus label.
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+ [2023-10-25 10:20:15,065] [WARNING] [root] 24 entries are missing rank phylum, but have family label.
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+ [2023-10-25 10:20:15,094] [WARNING] [root] 8759 entries are missing rank class, but have family label.
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+ [2023-10-25 10:20:15,123] [WARNING] [root] 111 entries are missing rank order, but have family label.
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+ [2023-10-25 10:20:15,233] [WARNING] [root] 67 entries are missing rank class, but have order label.
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+ [2023-10-25 10:20:15,254] [WARNING] [root] 253 entries have kingdom and species labels but no genus.
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+ [2023-10-25 10:20:15,254] [WARNING] [root] 253 entries have phylum and species labels but no genus.
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+ [2023-10-25 10:20:15,255] [WARNING] [root] 173 entries have class and species labels but no genus.
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+ [2023-10-25 10:20:15,255] [WARNING] [root] 253 entries have order and species labels but no genus.
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+ [2023-10-25 10:20:15,255] [WARNING] [root] 253 entries have family and species labels but no genus.
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+ [2023-10-25 10:20:16,644] [WARNING] [root] There are 755133 samples for which the species column may have genus and species.
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+ [2023-10-25 10:20:17,199] [WARNING] [root] 2470 species are labeled as '(unidentified)'.
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+ Output of Data Check for next iteration where taxon matching was performed (statistics.csv):
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+
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+ [2023-10-25 10:25:28,242] [WARNING] [root] There are 7 kingdoms instead of 3.
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+ [2023-10-25 10:25:29,234] [WARNING] [root] 14795 entries are missing rank kingdom, but have genus label.
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+ [2023-10-25 10:25:29,477] [WARNING] [root] 5824 entries are missing rank phylum, but have genus label.
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+ [2023-10-25 10:25:29,719] [WARNING] [root] 15763 entries are missing rank class, but have genus label.
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+ [2023-10-25 10:25:29,958] [WARNING] [root] 10550 entries are missing rank order, but have genus label.
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+ [2023-10-25 10:25:30,203] [WARNING] [root] 7539 entries are missing rank family, but have genus label.
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+ [2023-10-25 10:25:30,470] [WARNING] [root] 296 entries are missing rank kingdom, but have family label.
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+ [2023-10-25 10:25:30,495] [WARNING] [root] 272 entries are missing rank phylum, but have family label.
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+ [2023-10-25 10:25:30,520] [WARNING] [root] 753 entries are missing rank class, but have family label.
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+ [2023-10-25 10:25:30,545] [WARNING] [root] 395 entries are missing rank order, but have family label.
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+ [2023-10-25 10:25:30,590] [WARNING] [root] 156 entries are missing rank kingdom, but have order label.
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+ [2023-10-25 10:25:30,591] [WARNING] [root] 100 entries are missing rank phylum, but have order label.
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+ [2023-10-25 10:25:30,592] [WARNING] [root] 1187 entries are missing rank class, but have order label.
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+ [2023-10-25 10:25:30,637] [WARNING] [root] 74 entries have kingdom and species labels but no genus.
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+ [2023-10-25 10:25:30,644] [WARNING] [root] 74 entries have phylum and species labels but no genus.
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+ [2023-10-25 10:25:30,650] [WARNING] [root] 74 entries have class and species labels but no genus.
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+ [2023-10-25 10:25:30,656] [WARNING] [root] 74 entries have order and species labels but no genus.
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+ [2023-10-25 10:25:30,662] [WARNING] [root] 74 entries have family and species labels but no genus.
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+ [2023-10-25 10:25:31,992] [WARNING] [root] There are 158279 samples for which the species column may have genus and species.
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+ Added check for nulls in common column (wasn't an issue in the first iteration):
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+ [2023-10-25 11:39:11,384] [WARNING] [root] 915509 entries have null common. They are from ['EOL' 'BIOSCAN'].