TAG

https://github.com/standage/tag
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tag is a free open-source software package for analyzing genome annotation data, providing tools for...
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### Setting up Development Environment for tag Project

Source: https://github.com/standage/tag/blob/master/docs/dev.rst

Provides a quickstart guide to set up the development environment for the 'tag' project, including cloning the repository, setting up a virtual environment, installing dependencies, running tests, and configuring a pre-commit hook.

```bash
# Fork repo on GitHub then clone
git clone git@github.com:YourGithubUsername/tag.git
cd tag/

# Optional (but highly recommended): set up a virtual environment
virtualenv -p python3 env
echo "export PYTHONPATH=$(pwd)" >> env/bin/activate
source env/bin/activate  # Re-run this any time you return after launching a new terminal.

# Install Python libraries needed for testing and run the test suite
make devenv
make test
echo "make style" > .git/hooks/pre-commit

# Test the development CLI; end users will invoke `tag` instead of `./tagcli`
./tagcli -h
```

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### Install tag Python Package via pip

Source: https://github.com/standage/tag/blob/master/docs/install.rst

This snippet shows the standard way to install the tag package from the Python Package Index (PyPI) using the pip command. It ensures the most recent stable release is installed.

```bash
pip install tag
```

--------------------------------

### Install tag Python Package from GitHub

Source: https://github.com/standage/tag/blob/master/docs/install.rst

This snippet demonstrates how to install the latest unreleased code of the tag package directly from its development repository on GitHub using pip. This is useful for accessing the newest features or bug fixes.

```bash
pip install git+https://github.com/standage/tag.git
```

--------------------------------

### tag Package API Documentation Overview

Source: https://github.com/standage/tag/blob/master/docs/dev.rst

Describes the API of the 'tag' package, adhering to semantic versioning. It explains that changes to the command-line or Python interface require version bumps and that API documentation is generated directly from Python docstrings, with code examples in docstrings being executed during testing.

```APIDOC
The 'tag' package API adheres to semantic versioning (http://semver.org/).

Version Bumping:
- Minor version bump: For backwards-compatible additions to the CLI or Python interface.
- Major version bump: For API-breaking changes.

API Documentation Generation:
- Documentation is pulled directly from docstrings in class and module definitions.
- Any Python code within API docstrings is executed and evaluated via autodoc when the test suite is invoked.
```

--------------------------------

### Analyze Genomic Data Interactively with tag

Source: https://github.com/standage/tag/blob/master/docs/install.rst

This Python snippet illustrates how to use the tag library interactively within a Python interpreter. It demonstrates reading a GFF3 file, selecting features of a specific type (e.g., 'intron'), and filtering them based on length to print their slugs.

```python
import tag
reader = tag.reader.GFF3Reader(infilename='/data/genomes/mybug.gff3.gz')
for entry in tag.select.features(reader, type='intron'):
    if len(entry) > 100000:
        print(entry.slug)
```

--------------------------------

### Python API Modules and Classes for tag project

Source: https://github.com/standage/tag/blob/master/docs/api.rst

Overview of the core modules and classes available in the 'tag' Python API, including their purpose and the functionality they encapsulate. Each module's members are exposed for use, following semantic versioning.

```APIDOC
Module: tag
  Description: Core module for the tag project's Python API.
  Submodules:
    Module: tag.range
      Description: Provides functionality related to ranges.
      Members: All public members are exposed.
    Module: tag.comment
      Description: Handles comment-related operations.
      Members: All public members are exposed.
    Module: tag.directive
      Description: Manages directives within the tag system.
      Members: All public members are exposed.
    Module: tag.sequence
      Description: Deals with sequence-related operations.
      Members: All public members are exposed.
    Module: tag.feature
      Description: Provides functionality for handling features.
      Members: All public members are exposed.
    Module: tag.index
      Description: Manages indexing operations.
      Members: All public members are exposed.
    Module: tag.reader
      Description: Contains classes for reading data.
      Classes:
        Class: GFF3Reader
          Description: Reads GFF3 formatted files.
          Members: All public members are exposed.
    Module: tag.writer
      Description: Contains classes for writing data.
      Classes:
        Class: GFF3Writer
          Description: Writes GFF3 formatted files.
          Members: All public members are exposed.
    Module: tag.transcript
      Description: Provides functionality for handling transcripts.
      Members: All public members are exposed.
    Module: tag.select
      Description: Manages selection operations.
      Members: All public members are exposed.
    Module: tag.locus
      Description: Provides functionality for locus partitioning.
      Members: All public members are exposed.
    Module: tag.bae
      Description: Handles bacterial annotation evaluation.
      Members: All public members are exposed.
```

--------------------------------

### Compute Exons per Gene with tag

Source: https://github.com/standage/tag/blob/master/README.md

This Python snippet demonstrates how to use the 'tag' library to read a GFF3 file and iterate through gene features. For each gene, it identifies and counts the number of associated exon features, printing the result.

```Python
# Compute number of exons per gene
import tag
reader = tag.GFF3Reader(infilename='/data/genomes/mybug.gff3.gz')
for gene in tag.select.features(reader, type='gene'):
    exons = [feat for feat in gene if feat.type == exon]
    print('num exons:', len(exons))
```

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### Compute Exons Per Gene with tag in Python

Source: https://github.com/standage/tag/blob/master/docs/index.rst

This Python snippet demonstrates how to use the 'tag' library to read GFF3 annotation data and compute the number of exons for each gene. It utilizes `GFF3Reader` to parse the input file and `tag.select.features` to iterate through gene features, then filters for exons within each gene to count them.

```python
# Compute number of exons per gene
import tag
reader = tag.GFF3Reader(infilename='/data/genomes/mybug.gff3.gz')
for gene in tag.select.features(reader, type='gene'):
    exons = [feat for feat in gene if feat.type == exon]
    print('num exons:', len(exons))
```
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