gain package
Subpackages
- gain.annotation package
- Submodules
- gain.annotation.allele_score_annotator module
- gain.annotation.annotatable 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
- Submodules
- gain.binning.binners module
- gain.binning.cli module
- gain.binning.fragment_array_folds module
- gain.binning.fragment_binner module
- gain.binning.fragment_def module
- gain.binning.fragment_folds module
- gain.binning.fragment_grouping module
- gain.binning.h5_reader module
- gain.binning.position_fold module
- gain.binning.run_definition module
- gain.binning.view_cli module
- Module contents
- 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.batch_budget 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.exact_lengths module
- gain.genomic_resources.statistics.fragments module
- gain.genomic_resources.statistics.length_histogram module
- gain.genomic_resources.statistics.min_max module
- gain.genomic_resources.statistics.moments module
- gain.genomic_resources.statistics.percentages module
- gain.genomic_resources.statistics.png_bytes 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.annotation_pipeline_builder module
- gain.genomic_resources.testing.builders module
- gain.genomic_resources.testing.data_frame_builder module
- gain.genomic_resources.testing.extra_files module
- gain.genomic_resources.testing.faulty_filesystem module
- gain.genomic_resources.testing.gene_models_builder module
- gain.genomic_resources.testing.gene_set_collection_builder module
- gain.genomic_resources.testing.group_builder module
- gain.genomic_resources.testing.info_page_fixtures module
- gain.genomic_resources.testing.liftover_chain_builder module
- gain.genomic_resources.testing.resource_meta module
- gain.genomic_resources.testing.score_specs module
- gain.genomic_resources.testing.statistics 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.memo 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.grr package
- 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
- gain.utils.zulip_logging 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 trace / user_info logger
methods are registered as an import side effect of gain.utils.log_levels;
its docstring says how, and what a later foreign Logger.trace can and
cannot displace.
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 GainLogger. 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, which instantiates that same
class. Call sites therefore need no # type: ignore[attr-defined] for the
custom methods.