gain package
Subpackages
- gain.annotation package
- Submodules
- gain.annotation.allele_score_annotator module
- gain.annotation.annotatable module
- gain.annotation.annotate_columns module
- gain.annotation.annotate_doc module
- gain.annotation.annotate_tabular module
- gain.annotation.annotate_utils module
- gain.annotation.annotate_vcf module
- gain.annotation.annotation_config module
- gain.annotation.annotation_factory module
- gain.annotation.annotation_genomic_context_cli module
- gain.annotation.annotation_pipeline module
- gain.annotation.annotator_base module
- gain.annotation.chrom_mapping_annotator module
- gain.annotation.debug_annotator module
- gain.annotation.docker_annotator module
- gain.annotation.effect_annotator module
- gain.annotation.fragment_score_annotator module
- gain.annotation.gene_score_annotator module
- gain.annotation.gene_set_annotator module
- gain.annotation.genomic_score_annotator_base module
- gain.annotation.liftover_annotator module
- gain.annotation.normalize_allele_annotator module
- gain.annotation.pipeline_doc module
- gain.annotation.position_score_annotator module
- gain.annotation.prepare_tabular module
- gain.annotation.processing_pipeline module
- gain.annotation.record_to_annotatable module
- gain.annotation.simple_effect_annotator module
- gain.annotation.utils module
- gain.annotation.value_transform_eval module
- Module contents
- gain.binning package
- gain.dask package
- gain.effect_annotation package
- Subpackages
- gain.effect_annotation.effect_checkers package
- Submodules
- gain.effect_annotation.effect_checkers.coding module
- gain.effect_annotation.effect_checkers.effect_checker module
- gain.effect_annotation.effect_checkers.frame_shift module
- gain.effect_annotation.effect_checkers.intron module
- gain.effect_annotation.effect_checkers.promoter module
- gain.effect_annotation.effect_checkers.protein_change module
- gain.effect_annotation.effect_checkers.splice_site module
- gain.effect_annotation.effect_checkers.start_loss module
- gain.effect_annotation.effect_checkers.stop_loss module
- gain.effect_annotation.effect_checkers.utr module
- Module contents
- gain.effect_annotation.effect_checkers package
- Submodules
- gain.effect_annotation.annotation_effects module
- gain.effect_annotation.annotation_request module
- gain.effect_annotation.annotator module
- gain.effect_annotation.cli module
- gain.effect_annotation.effect module
- gain.effect_annotation.gene_codes module
- gain.effect_annotation.variant module
- Module contents
- Subpackages
- gain.gene_scores package
- gain.gene_sets package
- gain.genomic_resources package
- Subpackages
- gain.genomic_resources.gene_models package
- Submodules
- gain.genomic_resources.gene_models.default_attributes module
- gain.genomic_resources.gene_models.gene_models module
- gain.genomic_resources.gene_models.gene_models_factory module
- gain.genomic_resources.gene_models.parsers module
- gain.genomic_resources.gene_models.record_cells module
- gain.genomic_resources.gene_models.serialization module
- gain.genomic_resources.gene_models.to_gpf_gene_models_format module
- gain.genomic_resources.gene_models.transcript_models module
- Module contents
- gain.genomic_resources.genomic_position_table package
- Submodules
- gain.genomic_resources.genomic_position_table.index_columns module
- gain.genomic_resources.genomic_position_table.line module
- gain.genomic_resources.genomic_position_table.record module
- gain.genomic_resources.genomic_position_table.table module
- gain.genomic_resources.genomic_position_table.table_bigwig module
- gain.genomic_resources.genomic_position_table.table_inmemory module
- gain.genomic_resources.genomic_position_table.table_tabix module
- gain.genomic_resources.genomic_position_table.table_vcf module
- gain.genomic_resources.genomic_position_table.utils module
- Module contents
- gain.genomic_resources.genomic_scores package
- Submodules
- gain.genomic_resources.genomic_scores.aggregation module
- gain.genomic_resources.genomic_scores.allele module
- gain.genomic_resources.genomic_scores.base module
- gain.genomic_resources.genomic_scores.builders module
- gain.genomic_resources.genomic_scores.chrom_lengths module
- gain.genomic_resources.genomic_scores.fragment module
- gain.genomic_resources.genomic_scores.position module
- gain.genomic_resources.genomic_scores.records module
- gain.genomic_resources.genomic_scores.value_extraction module
- Module contents
- gain.genomic_resources.implementations package
- Subpackages
- Submodules
- gain.genomic_resources.implementations.ann_data_resource_impl module
- gain.genomic_resources.implementations.annotation_pipeline_impl module
- gain.genomic_resources.implementations.basic_resource_impl module
- gain.genomic_resources.implementations.data_frame_resource_impl module
- gain.genomic_resources.implementations.gene_models_impl module
- gain.genomic_resources.implementations.liftover_chain_impl module
- gain.genomic_resources.implementations.reference_genome_impl module
- Module contents
- gain.genomic_resources.statistics package
- Submodules
- gain.genomic_resources.statistics.alleles module
- gain.genomic_resources.statistics.base_statistic module
- gain.genomic_resources.statistics.chart_style module
- gain.genomic_resources.statistics.coverage module
- gain.genomic_resources.statistics.fragments module
- gain.genomic_resources.statistics.indel_lengths module
- gain.genomic_resources.statistics.length_histogram module
- gain.genomic_resources.statistics.min_max module
- gain.genomic_resources.statistics.percentages module
- gain.genomic_resources.statistics.record_validation module
- gain.genomic_resources.statistics.region_fold module
- Module contents
- gain.genomic_resources.testing package
- Submodules
- gain.genomic_resources.testing.ann_data_builder module
- gain.genomic_resources.testing.builders module
- gain.genomic_resources.testing.data_frame_builder module
- gain.genomic_resources.testing.faulty_filesystem module
- gain.genomic_resources.testing.gene_models_builder module
- gain.genomic_resources.testing.group_builder module
- gain.genomic_resources.testing.info_page_fixtures module
- gain.genomic_resources.testing.resource_meta module
- gain.genomic_resources.testing.score_specs module
- Module contents
- gain.genomic_resources.gene_models package
- Submodules
- gain.genomic_resources.aggregators module
- gain.genomic_resources.allele_classification module
- gain.genomic_resources.ann_data_10x module
- gain.genomic_resources.ann_data_resource module
- gain.genomic_resources.bigwig_scores module
- gain.genomic_resources.cached_repository module
- gain.genomic_resources.cli module
- gain.genomic_resources.cli_cache_repo module
- gain.genomic_resources.cli_dvc module
- gain.genomic_resources.cli_errors module
- gain.genomic_resources.cli_list module
- gain.genomic_resources.data_frame_resource module
- gain.genomic_resources.draw_score_histograms module
- gain.genomic_resources.dvc module
- gain.genomic_resources.fsspec_protocol module
- gain.genomic_resources.genomic_context module
- gain.genomic_resources.genomic_context_base module
- gain.genomic_resources.genomic_context_cli module
- gain.genomic_resources.group_repository module
- gain.genomic_resources.histogram module
- gain.genomic_resources.liftover_chain module
- gain.genomic_resources.reference_genome module
- gain.genomic_resources.repository module
- gain.genomic_resources.repository_factory module
- gain.genomic_resources.resource_errors module
- gain.genomic_resources.resource_implementation module
- gain.genomic_resources.resource_query module
- gain.genomic_resources.resource_types module
- gain.genomic_resources.score_def module
- gain.genomic_resources.score_filter module
- gain.genomic_resources.score_implementation module
- gain.genomic_resources.score_resource module
- gain.genomic_resources.utils module
- gain.genomic_resources.variant_utils module
- gain.genomic_resources.vcf_scores module
- Module contents
- Subpackages
- gain.task_graph package
- Submodules
- gain.task_graph.base_executor module
- gain.task_graph.cache module
- gain.task_graph.cli_tools module
- gain.task_graph.dask_executor module
- gain.task_graph.dask_run_state module
- gain.task_graph.demo_graphs_cli module
- gain.task_graph.executor module
- gain.task_graph.graph module
- gain.task_graph.logging module
- gain.task_graph.process_pool_executor module
- gain.task_graph.sequential_executor module
- gain.task_graph.work_dir module
- Module contents
- gain.templates package
- gain.testing package
- gain.utils package
- Submodules
- gain.utils.chromosome_order module
- gain.utils.cnv_utils module
- gain.utils.dae_utils module
- gain.utils.debug_closing module
- gain.utils.dict_utils module
- gain.utils.fs_utils module
- gain.utils.helpers module
- gain.utils.log_levels module
- gain.utils.log_safety module
- gain.utils.processing_pipeline module
- gain.utils.regions module
- gain.utils.resource_id_order module
- gain.utils.stats_collection module
- gain.utils.stringify module
- gain.utils.url_redaction module
- gain.utils.variant_utils module
- gain.utils.verbosity_configuration module
- Module contents
Submodules
gain.logging module
Drop-in replacement for stdlib logging with GAIn’s custom levels.
Import this instead of stdlib logging to guarantee TRACE and USER_INFO are registered before any logger is created:
from gain import logging logger = logging.getLogger(__name__) logger.trace(“fine-grained diagnostic”) logger.user_info(“message for the end user”)
Everything exported by stdlib logging is re-exported here (via a star
import that honours stdlib’s __all__), so this module tracks the stdlib
surface across Python versions instead of a hand-maintained name list. The
config and handlers submodules are re-exported too, so
from gain import logging; logging.config.dictConfig(...) keeps working.
The custom TRACE / USER_INFO levels (and the Logger.trace /
Logger.user_info methods) are registered as an import side effect of
gain.utils.log_levels, which monkeypatches logging.Logger globally so
that every logger — including the root logger and any already created — gains
the methods at runtime.
The same import installs the url-userinfo log-record seam of
gain.utils.url_redaction (ADR 0023, gain#1363). Both bootstraps also run
from gain/__init__, so importing anything under gain is enough.
For type checkers, getLogger is declared to return a Logger subclass
advertising .trace / .user_info. This is a pure typing shim: it is
declared before the star import so the type checker adopts the richer return
type, while at runtime the star import rebinds getLogger to the stdlib
function (identical behaviour — the methods come from the monkeypatch above).
Call sites therefore need no # type: ignore[attr-defined] for the custom
methods.