Quick Start¶

Build a vector database¶

Build a vector database from a FASTA file

from taxotagger import ProjectConfig
from taxotagger import TaxoTagger

config = ProjectConfig()
tt = TaxoTagger(config)

tt.create_db('data/database.fasta') # (1)!

The data is available in the repo.

Run the code above, you will see the following messages:

[2024-08-22 09:45:42] INFO     Embedding the DNA sequences in data/database.fasta using the model MycoAI-CNN                              taxotagger.py:69
Downloading https://zenodo.org/records/10904344/files/MycoAI-CNN.pt to ~/.cache/mycoai
Downloading MycoAI-CNN.pt ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 0:00:00
[2024-08-22 09:46:06] INFO     Loading model MycoAI-CNN from ~/.cache/mycoai/MycoAI-CNN.pt                                                utils.py:97
[2024-08-22 09:46:12] INFO     Creating vector database for the DNA sequences in data/database.fasta at ~/.cache/mycoai/MycoAI-CNN.db     taxotagger.py:199
[2024-08-22 09:47:21] INFO     Database created successfully at ~/.cache/mycoai/MycoAI-CNN.db                                             taxotagger.py:230

By default, the ~/.cache/mycoai folder is used to store the vector database and the embedding model. The MycoAI-CNN.pt model is automatically downloaded to this folder if it is not there, and the vector database is created and named after the model.

You can use a different embedding model by specifying the model name:

Using a different embedding model

tt.create_db('data/database.fasta', model_id='other_model_name') # (1)!

Just the name of the model without the .pt extension.

You may want to integrate TaxoTagger with your own embedding model. See the Custom Embedding Models guide for more details.

Semantic searching¶

After building the vector database, you can conduct a semantic search with a query FASTA file:

Conduct a semantic search with FASTA file

from taxotagger import ProjectConfig
from taxotagger import TaxoTagger

config = ProjectConfig()
tt = TaxoTagger(config)

res = tt.search('data/query.fasta', limit=1) # (1)!

The limit parameter specifies the number of top results to return for each query sequence. If you want to return the top 3 results, you can set limit=3.

The data/query.fasta file contains two query sequences:

>KY106088|k__Fungi;p__Ascomycota;c__Saccharomycetes;o__Saccharomycetales;f__Saccharomycetaceae;g__Zygotorulaspora;s__Zygotorulaspora_mrakii|SH1312607.09FU
GTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTATAGAAAAAAATGGAAGGGCCATGCGCTTAATTGCGCGGGCCCTCTCTTATTCACACGATGGAGACGAATATCTTCCTGCTTAGGGGCACGAGGCTTGGACCGAGTGGCCCGGCAGACACAAACACAAACAAATTTTTTTTGAATTTACGAATTAAAAAGAGTCAAAAACAAAATAAAAACAAAATATACCAAAACTTTCAACAACGGATCTCTTGGTTCTCGCACCGATGAAGAACGCAGCGAAATGCGATACGTAATGTGAATTGCAGAATTCCGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTTGGTATTCCAGGGGGCATGCCTGTTTGAGCGTCATTTCCTTCTCAAACACACGGTGTTTGGTGGTGAGTGATACTCTTTCTGGGAGTTAGCTTGAAAGTGTGAGCCCGTGGACTGCTCTTTTTGCTGTAGGCGGAAAAAAGTCGTGCTAGGTAACCACCAACTCGACGGACGTTCGGCCGACAAGGAAAACGGGGCGGTCGGGTCAACAGACACACATCAACGCTTGACCTCAAATCAGGTAGGAATACCCGCTGAACTTAAGCATATCAATAAGCGGA
>KY106087|k__Fungi;p__Ascomycota;c__Saccharomycetes;o__Saccharomycetales;f__Saccharomycetaceae;g__Zygotorulaspora;s__Zygotorulaspora_mrakii|SH1312607.09FU
AACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTATAGAAAAAAATGGAAGGGCCATGCGCTTAATTGCGCGGGCCCTCTCTTATTCACACGATGGAGACGAATATCTTCCTGCTTAGGGGCACGAGGCTTGGACCGAGTGGCCCGGCAGACACAAACACAAACAAATTTTTTTTGAATTTACGAATTAAAAAGAGTCAAAAACAAAATAAAAACAAAATATACCAAAACTTTCAACAACGGATCTCTTGGTTCTCGCACCGATGAAGAACGCAGCGAAATGCGATACGTAATGTGAATTGCAGAATTCCGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTTGGTATTCCAGGGGGCATGCCTGTTTGAGCGTCATTTCCTTCTCAAACACACGGTGTTTGGTGGTGAGTGATACTCTTTCTGGGAGTTAGCTTGAAAGTGTGAGCCCGTGGACTGCTCTTTTTGCTGTAGGCGGAAAAAAGTCGTGCTAGGTAACCACCAACTCGACGGACGTTCGGCCGACAAGGAAAACGGGGCGGTCGGGTCAACAGACACACATCAACGCTTGACCTCAAATCAGGTAGGAATACCCGCTGAACTTAAGCATATCAA

The search results res will be a dictionary with taxonomic level names as keys and matched results as values for each of the two query sequences. For example, res['phylum'] will look like:

Search results for phylum

[
    [{"id": "KY106088", "distance": 1.0, "entity": {"phylum": "Ascomycota"}}],
    [{"id": "KY106087", "distance": 0.9999998807907104, "entity": {"phylum": "Ascomycota"}}]
]

The first inner list is the top results for the first query sequence, and the second inner list is the top results for the second query sequence.

The id field is the sequence ID of the matched sequence. The distance field is the cosine similarity between the query sequence and the matched sequence with a value between 0 and 1, the closer to 1, the more similar. The entity field is the taxonomic information of the matched sequence.

We can see that the top 1 results for both query sequences are exactly themselves. This is because the query sequences are also in the database. You can try with different query sequences to see the search results.

Project Configuration¶

The ProjectConfig class is used to configure the project settings.

You can change the settings by creating an instance of the class and setting the attributes:

Change project settings after creating the instance

from taxotagger import ProjectConfig

config = ProjectConfig()

# Change cache folder
config.mycoai_home = '~/temp_dir' 

# Use GPU for computation
config.device = 'cuda'

# Force re-download and reload embedding model
config.force_reload = True

# Set the log level to DEBUG
config.log_level = 'DEBUG'

# Log to a file
config.log_file = '~/taxotagger.log'

# Do not log to console
config.log_to_console = False

Or you can set the attributes directly when creating the instance:

Change project settings when creating the instance

from taxotagger import ProjectConfig

config = ProjectConfig(
    mycoai_home='~/temp_dir',
    device='cuda',
    force_reload=True,
    log_level='DEBUG',
    log_file='~/taxotagger.log',
    log_to_console=False
)

After creating the instance, you can pass the config object to the TaxoTagger class to use the settings:

Pass the config object to the TaxoTagger class

from taxotagger import TaxoTagger

tt = TaxoTagger(config)

Tip

The settings are read only when creating the TaxoTagger instance.

So if you change the settings after creating the instance, the changes will not take effect. You need to create a new TaxoTagger instance with the updated settings.