Genomic resources
GAIn provides a Python interface for accessing and working with genomic resources stored in Genomic Resource Repositories (GRRs). Through this interface, users can retrieve genomic sequences, inspect gene models, query genomic scores, and load datasets for further analysis using Python.
Each resource in a GRR is identified by a resource ID and has a definition describing its type, associated files, and other properties. GAIn provides Python functions for locating these resources and creating objects with methods appropriate to each resource type. For example, a reference genome object provides methods for retrieving DNA sequences, while a genomic score object allows users to retrieve scores for genomic positions, alleles, or intervals.
This section focuses on accessing and using existing genomic resources through Python. Defining new resources, configuring their properties in genomic_resource.yaml, and managing them with grr_manage are covered separately in the Genomic resources and repositories documentation.
The following chapters describe the Python interfaces for different types of genomic resources, beginning with repositories and resources themselves. Readers unfamiliar with the Python interface may first consult the Overview and examples page, which provides practical examples.