Datasets:
Ahmed Moustafa
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README.md
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@@ -62,7 +62,7 @@ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
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This modified version (gg_2024_09) was created by [the Systems Genomics Lab](https://github.com/systems-genomics-lab) for use with DeepTaxa. The Greengenes database, downloaded from https://ftp.microbio.me/greengenes_release/2022.10/, was processed as follows:
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1. The original dataset, containing 23,450,269 sequences, was downloaded.
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2. Missing taxonomic classifications were filled with "Unclassified" or derived labels. For each sequence, the taxonomy table's ranks (e.g.,
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- If no prior rank had a valid value, the field was left empty.
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- If the previous rank's value included "Unclassified," that value was copied to the current rank.
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- Otherwise, the field was set to "Unclassified_" followed by the previous rank's value (e.g., "Unclassified_Proteobacteria" for a missing class after phylum "Proteobacteria").
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This modified version (gg_2024_09) was created by [the Systems Genomics Lab](https://github.com/systems-genomics-lab) for use with DeepTaxa. The Greengenes database, downloaded from https://ftp.microbio.me/greengenes_release/2022.10/, was processed as follows:
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1. The original dataset, containing 23,450,269 sequences, was downloaded.
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+
2. Missing taxonomic classifications were filled with "Unclassified" or derived labels. For each sequence, the taxonomy table's ranks (e.g., domain, phylum, class) were processed sequentially. If a rank was empty or contained only whitespace:
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- If no prior rank had a valid value, the field was left empty.
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- If the previous rank's value included "Unclassified," that value was copied to the current rank.
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- Otherwise, the field was set to "Unclassified_" followed by the previous rank's value (e.g., "Unclassified_Proteobacteria" for a missing class after phylum "Proteobacteria").
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