`.subset_to` Behaviour

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Understanding the .subset_to Behaviour in Genomic Variants Library (GVL)

The Genomic Variants Library (GVL) is a powerful tool for working with genomic data. One of its key features is the ability to subset datasets based on various parameters, including samples and sequences. However, as we will explore in this article, the behavior of the .subset_to method can be nuanced and dependent on the specific parameters used. In this article, we will delve into the unexpected behavior of .subset_to when subsetting samples with the "haplotypes" and "reference" parameters.

The .subset_to method is used to subset a dataset based on a given parameter. In the context of GVL, this method can be used to subset samples, sequences, or both. The method takes a list of values as input, which specifies the subset of interest. For example, to subset a dataset to include only the first sample, you would use the following code:

ds = (
    gvl.Dataset.open(ds_path, reference=reference)
    .subset_to(samples=[0])
)

This code will return a new dataset that includes only the first sample.

Subsetting Samples with "Haplotypes" Parameter

When subsetting samples with the "haplotypes" parameter, the expected behavior is to return a dataset with two sequences, one for each haplotype in the sample. This is because haplotypes are typically diploid, meaning they consist of two distinct sequences. To demonstrate this, let's consider the following code:

ds = (
    gvl.Dataset.open(ds_path, reference=reference)
    .with_seqs("haplotypes")
    .subset_to(samples=[0])
    .with_len(2**18)
)

As expected, this code returns a dataset with two sequences, one for each haplotype in the sample.

Subsetting Samples with "Reference" Parameter

However, when subsetting samples with the "reference" parameter, the behavior is different. Instead of returning a dataset with two sequences, one for each haplotype in the sample, the method returns a dataset with only one sequence. This is because the reference is technically haploid, meaning it consists of a single sequence. To demonstrate this, let's consider the following code:

ds = (
    gvl.Dataset.open(ds_path, reference=reference)
    .with_seqs("reference")
    .subset_to(samples=[0])
    .with_len(2**18)
)

As shown in the code, the resulting dataset has only one sequence.

Is the Reference Technically Haploid?

So, is the reference technically haploid? The answer is yes. In the context of GVL, the reference is considered haploid because it consists of a single sequence. This is in contrast to haplotypes, which are typically diploid and consist of two distinct sequences.

In conclusion, the behavior of the .subset_to method in GVL can be nuanced and dependent on the specific parameters used. When subsetting samples with the "haplotypes" parameter, the method returns a dataset with two sequences, one for each haplotype in the sample. However, when subsetting samples with the "reference" parameter, the method returns a dataset with only one sequence, due to the reference being technically haploid. Understanding this behavior is essential for working effectively with genomic data in GVL.

Future work could involve exploring other parameters that can be used with the .subset_to method, such as subsetting samples based on specific variants or annotations. Additionally, further investigation into the behavior of the method when working with different types of genomic data could provide valuable insights into the capabilities and limitations of GVL.

Here are some code examples that demonstrate the behavior of the .subset_to method:

# Subsetting samples with "haplotypes" parameter
ds = (
    gvl.Dataset.open(ds_path, reference=reference)
    .with_seqs("haplotypes")
    .subset_to(samples=[0])
    .with_len(2**18)
)

# Subsetting samples with "reference" parameter
ds = (
    gvl.Dataset.open(ds_path, reference=reference)
    .with_seqs("reference")
    .subset_to(samples=[0])
    .with_len(2**18)
)

These code examples demonstrate the expected behavior of the .subset_to method when subsetting samples with the "haplotypes" and "reference" parameters.

Note: The code examples and references provided are for illustrative purposes only and may not reflect the actual behavior of the .subset_to method in GVL.
Frequently Asked Questions (FAQs) about .subset_to Behaviour in Genomic Variants Library (GVL)

Q: What is the .subset_to method in GVL?

A: The .subset_to method is a powerful tool in GVL that allows you to subset a dataset based on various parameters, including samples and sequences.

Q: What are the different parameters that can be used with the .subset_to method?

A: The .subset_to method can be used with the following parameters:

  • samples: Subsets the dataset to include only specific samples.
  • seqs: Subsets the dataset to include only specific sequences.
  • variants: Subsets the dataset to include only specific variants.
  • annotations: Subsets the dataset to include only specific annotations.

Q: What is the expected behavior of the .subset_to method when subsetting samples with the "haplotypes" parameter?

A: When subsetting samples with the "haplotypes" parameter, the expected behavior is to return a dataset with two sequences, one for each haplotype in the sample.

Q: What is the expected behavior of the .subset_to method when subsetting samples with the "reference" parameter?

A: When subsetting samples with the "reference" parameter, the expected behavior is to return a dataset with only one sequence, due to the reference being technically haploid.

Q: Why does the .subset_to method return a different shape when subsetting samples with the "reference" parameter compared to the "haplotypes" parameter?

A: The .subset_to method returns a different shape when subsetting samples with the "reference" parameter compared to the "haplotypes" parameter because the reference is technically haploid, meaning it consists of a single sequence, whereas haplotypes are typically diploid and consist of two distinct sequences.

Q: Can I use the .subset_to method to subset samples based on specific variants or annotations?

A: Yes, you can use the .subset_to method to subset samples based on specific variants or annotations. However, this requires additional parameters and may have different expected behaviors.

Q: What are some common use cases for the .subset_to method?

A: Some common use cases for the .subset_to method include:

  • Subsetting a dataset to include only specific samples or sequences.
  • Identifying specific variants or annotations in a dataset.
  • Analyzing the relationship between different samples or sequences in a dataset.

Q: How can I troubleshoot issues with the .subset_to method?

A: To troubleshoot issues with the .subset_to method, you can try the following:

  • Check the documentation for the .subset_to method to ensure you are using it correctly.
  • Verify that the input parameters are correct and match the expected behavior.
  • Use debugging tools or print statements to inspect the intermediate results and identify any issues.

Q: Where can I find more information about the .subset_to method and GVL?

A: You can find more information about the .subset_to method and GVL in the following resources:

Note: The FAQs provided are for illustrative purposes only and may not reflect the actual behavior of the .subset_to method in GVL.