Cleaning up

README.md

@@ -19,15 +19,20 @@ size_categories:
 This dataset contains 16S rRNA gene sequences with hierarchical taxonomic annotations, designed for training and evaluating models like DeepTaxa. It is a processed version of the Greengenes database, widely used in microbiome research.
 
 ## Dataset Details
-- **Files**:
-  - `gg_2024_09_training.fna.gz`: Training sequences (FASTA)
-  - `gg_2024_09_training.tsv.gz`: Training labels (TSV)
-  - `gg_2024_09_testing.fna.gz`: Testing sequences (FASTA)
-  - `gg_2024_09_testing.tsv.gz`: Testing labels (TSV)
-  - `gg_2024_09_training_ids.txt`: Training sequence IDs
-  - `gg_2024_09_testing_ids.txt`: Testing sequence IDs
-- **Format**: FASTA (sequences), TSV (labels with 7 taxonomic levels)
-- **Source**: Derived from Greengenes (DeSantis et al., 2006)
+
+The dataset includes the following files:
+
+| File Name                        | Type                  | Number of Sequences | Size         |
+|----------------------------------|-----------------------|---------------------|--------------|
+| `gg_2024_09_training.fna.gz`     | FASTA (sequences)     | 277,336             | ~96.4 MB     |
+| `gg_2024_09_training.tsv.gz`     | TSV (taxonomy labels) | 277,336             | ~2.6 MB      |
+| `gg_2024_09_testing.fna.gz`      | FASTA (sequences)     | 69,335              | ~24.1 MB     |
+| `gg_2024_09_testing.tsv.gz`      | TSV (taxonomy labels) | 69,335              | ~0.8 MB      |
+| `gg_2024_09_training_ids.txt`    | Text (sequence IDs)   | 277,336             | -            |
+| `gg_2024_09_testing_ids.txt`     | Text (sequence IDs)   | 69,335              | -            |
+
+- **Format**: FASTA for sequences (compressed), TSV for labels with 7 taxonomic levels (compressed).
+- **Source**: Derived from Greengenes (DeSantis et al., 2006), downloaded from https://ftp.microbio.me/greengenes_release/2022.10/
 
 ## Usage
 Use with DeepTaxa:
@@ -57,7 +62,18 @@ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
 
 ### Modifications
 
-This modified version (gg_2024_09) was created by the Systems Genomics Lab for use with DeepTaxa. The modifications include splitting the dataset into training and testing sets and adding ID files.
+This modified version (gg_2024_09) was created by the Systems Genomics Lab for use with DeepTaxa. The Greengenes database, downloaded from https://ftp.microbio.me/greengenes_release/2022.10/, was processed as follows:
+1. The original dataset, containing 23,450,269 sequences, was downloaded.
+2. Missing taxonomic classifications were filled with "Unclassified."
+3. Sequences were filtered to retain only those with at least 300 nucleotides, resulting in 354,023 sequences.
+4. Sequence IDs were extracted, and the taxonomy table was filtered to match these IDs, yielding 346,671 entries (7,352 IDs not found were noted).
+5. A clean ID list was generated from the filtered taxonomy table (346,671 IDs).
+6. Sequences were filtered to match the clean ID list, retaining 346,671 sequences.
+7. The dataset was split into training (277,336 sequences) and testing (69,335 sequences) sets using an 80:20 ratio and a fixed random seed.
+8. Training and testing sequence IDs were extracted (277,336 and 69,335 IDs, respectively).
+9. The taxonomy table was filtered to create separate training (277,336 rows) and testing (69,335 rows) label files.
+
+These steps ensured the dataset was cleaned, filtered, and split for use with DeepTaxa.
 
 Copyright (c) 2025, Systems Genomics Lab
 
@@ -77,4 +93,5 @@ For the dataset:
 For DeepTaxa: See [GitHub](https://github.com/systems-genomics-lab/deeptaxa).
 
 ## Contact
-Report issues on [GitHub](https://github.com/systems-genomics-lab/deeptaxa/issues).
+Report issues on [GitHub](https://github.com/systems-genomics-lab/deeptaxa/issues).
+

gg_2024_09_testing.fna.gz

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:e02db8ad3d3790f542bf7efda7cecbdeb631472eadb3eef4a382a61f39742183
-size 8100351
+oid sha256:d79347cb231edc72371c20daa8384581a1e6fbb9fa8ad6e172a3eecba29b5709
+size 25272074

gg_2024_09_testing.tsv.gz

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:f5848fbbe50db51a0f2ecac830230677cedfa9df691da2356bfa61bc598f7835
-size 306233
+oid sha256:d5268e7980ce81a39a521e22ff6078f622843c792682e7f95519188475c6d6bb
+size 828270

gg_2024_09_training.fna.gz

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:938c51e8b6e5e45dbdd2798f40973ca51d4d430f9f88d7af0fe58f67dc9eaea7
-size 72838056
+oid sha256:277d990a1e476c149ba219fef69089a892e07b3271e9bc18cb7d58a0cec1214d
+size 101082158

gg_2024_09_training.tsv.gz

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:329f85ca57ceeabe2826f84368c5a7e752556d245cc8fa6e74436ab874a9695a
-size 2018957
+oid sha256:266a90b974562e09f6467c96ce73c4ca09042ee896786aee211d08ee031ed83b
+size 2756664