src.core package

Subpackages

• src.core.analyzer package
  • Submodules
  • src.core.analyzer.adapter_trimmer module
    • AdapterTrimmer
      • AdapterTrimmer.perform()
      • AdapterTrimmer._abc_impl
      • AdapterTrimmer._is_protocol
  • src.core.analyzer.amplicon_coverage_computer module
    • PositionNotFoundError
    • AmpliconCoverageDataPreparator
      • AmpliconCoverageDataPreparator.generate_mpileup()
      • AmpliconCoverageDataPreparator.count_region_coverage()
      • AmpliconCoverageDataPreparator.count_indels()
      • AmpliconCoverageDataPreparator.count_target_char()
      • AmpliconCoverageDataPreparator.count_variant_coverage()
      • AmpliconCoverageDataPreparator.perform()
      • AmpliconCoverageDataPreparator._abc_impl
      • AmpliconCoverageDataPreparator._is_protocol
  • src.core.analyzer.annotation_adapter module
    • IAnnotationAdapter
      • IAnnotationAdapter.annotate()
      • IAnnotationAdapter._abc_impl
      • IAnnotationAdapter._is_protocol
    • SnpEffAnnotationAdapter
      • SnpEffAnnotationAdapter.annotate()
      • SnpEffAnnotationAdapter._abc_impl
      • SnpEffAnnotationAdapter._is_protocol
  • src.core.analyzer.bam_grouper module
    • BamGrouper
      • BamGrouper.perform()
      • BamGrouper._abc_impl
      • BamGrouper._is_protocol
  • src.core.analyzer.bqsr_performer module
    • BQSRPerformer
      • BQSRPerformer.perform()
      • BQSRPerformer._abc_impl
      • BQSRPerformer._is_protocol
  • src.core.analyzer.i_data_preparator module
    • IDataPreparator
      • IDataPreparator.perform()
      • IDataPreparator._abc_impl
      • IDataPreparator._is_protocol
  • src.core.analyzer.i_variant_caller module
    • IVariantCaller
      • IVariantCaller.call_variant()
      • IVariantCaller._abc_impl
      • IVariantCaller._is_protocol
  • src.core.analyzer.primer_cutter module
    • CutPrimers
      • CutPrimers.perform()
      • CutPrimers._abc_impl
      • CutPrimers._is_protocol
    • PTrimmer
      • PTrimmer.perform()
      • PTrimmer._abc_impl
      • PTrimmer._is_protocol
    • PrimerCutter
      • PrimerCutter.create_primer_cutter()
  • src.core.analyzer.sequence_aligner module
    • SequenceAligner
      • SequenceAligner.perform()
      • SequenceAligner._abc_impl
      • SequenceAligner._is_protocol
    • BWAAligner
      • BWAAligner.perform()
      • BWAAligner._abc_impl
      • BWAAligner._is_protocol
  • src.core.analyzer.variant_caller module
    • VariantCaller
      • VariantCaller.configurator
      • VariantCaller.call_variant()
      • VariantCaller._abc_impl
      • VariantCaller._is_protocol
    • PiscesVariantCaller
      • PiscesVariantCaller.call_variant()
      • PiscesVariantCaller.call_variant()
      • PiscesVariantCaller._abc_impl
      • PiscesVariantCaller._is_protocol
    • UnifiedGenotyperVariantCaller
      • UnifiedGenotyperVariantCaller.call_variant()
      • UnifiedGenotyperVariantCaller.call_variant()
      • UnifiedGenotyperVariantCaller._abc_impl
      • UnifiedGenotyperVariantCaller._is_protocol
    • FreebayesVariantCaller
      • FreebayesVariantCaller.call_variant()
      • FreebayesVariantCaller.call_variant()
      • FreebayesVariantCaller._abc_impl
      • FreebayesVariantCaller._is_protocol
  • src.core.analyzer.variant_caller_factory module
    • VariantCallerFactory
      • VariantCallerFactory.create_caller()
  • Module contents
• src.core.configurator package
  • Submodules
  • src.core.configurator.argument_parser module
    • IArgumentParser
      • IArgumentParser.parse()
      • IArgumentParser._abc_impl
      • IArgumentParser._is_protocol
    • ArgumentParser
      • ArgumentParser.parse()
      • ArgumentParser._abc_impl
      • ArgumentParser._is_protocol
  • src.core.configurator.config_loader module
    • IConfigLoader
      • IConfigLoader.load()
      • IConfigLoader._abc_impl
      • IConfigLoader._is_protocol
    • ConfigLoader
      • ConfigLoader.load()
      • ConfigLoader._abc_impl
      • ConfigLoader._is_protocol
  • src.core.configurator.configuration_error module
    • ConfigurationError
      • ConfigurationError.message
  • src.core.configurator.logging_configurator module
    • ILoggingConfigurator
      • ILoggingConfigurator.set_logger()
      • ILoggingConfigurator._abc_impl
      • ILoggingConfigurator._is_protocol
    • LoggingConfigurator
      • LoggingConfigurator._abc_impl
      • LoggingConfigurator._is_protocol
      • LoggingConfigurator.set_logger()
  • src.core.configurator.path_validator module
    • IPathValidator
      • IPathValidator.verify_path()
      • IPathValidator._abc_impl
      • IPathValidator._is_protocol
    • PathValidator
      • PathValidator.verify_path()
      • PathValidator._abc_impl
      • PathValidator._is_protocol
  • Module contents

Submodules

src.core.base module

This module provides utility classes and functions for system command execution, file management, archive extraction, platform detection, and logging.

Main components include:

• SingletonMeta:

  A metaclass implementing the singleton pattern.

• LoggerMixin:

  A mixin class to add logging capabilities to other classes.

• ICommandExecutor:

  Protocol defining an interface for command execution.

• CommandExecutor:

  A class to execute system commands via a callable.

• execute:

  Utility function to run commands with an executor.

• touch:

  Creates or updates the timestamp of a file.

• insert_processing_infix:

  Inserts a string into a filename before its extension.

• extract_archive:

  Extracts various archive formats (zip, tar, gzip).

• get_platform:

  Detects the current operating system platform.

This module facilitates building robust scripts and applications that require system command execution, file handling, archive processing, and environment detection.

class src.core.base.SingletonMeta

Bases: type

Metaclass implementing the Singleton pattern.

Ensures that only one instance of a class is created.

_instances = {}

class src.core.base.LoggerMixin(logger: Logger = None)

Bases: object

Mixin class providing logging capabilities.

logger

Custom logger instance.

Type:

logging.Logger

set_logger(logger: Logger = None) → None

Sets the logger instance.

Parameters:

logger (Optional[logging.Logger]) – New logger to set.

class src.core.base.ICommandExecutor(*args, **kwargs)

Bases: Protocol

Protocol for command executor classes.

Defines the interface for executing system commands.

run(command: list[str] | str | dict[str, str]) → bool

Executes a command.

Parameters:

command (Union[list[str], str, dict[str, str]]) – Command to execute.

_abc_impl = <_abc._abc_data object>

_is_protocol = True

class src.core.base.CommandExecutor(caller: callable = <built-in function system>, logger: ~logging.Logger | None = None)

Bases: LoggerMixin, ICommandExecutor

Executes system commands using a provided callable.

caller

Function that executes commands, defaults to os.system.

Type:

callable

logger

Logger instance for logging.

Type:

logging.Logger

run(command: list[str] | str | dict[str, str]) → bool

Executes the given command.

Parameters:

command (Union[list[str], str, dict[str, str]]) – Command to run.

Returns:

True if command executed successfully, False otherwise.

Return type:

bool

_abc_impl = <_abc._abc_data object>

_is_protocol = False

src.core.base.execute(executor, command) → None

Executes a command using the provided executor.

Parameters:

• executor (Union[ICommandExecutor, callable]) – Executor object or callable.

• command (Union[list[str], str, dict[str, str]]) – Command to execute.

src.core.base.touch(path: PathLike) → None

Creates an empty file or updates the timestamp if it exists.

Parameters:

path (PathLike[AnyStr]) – Path to the file.

src.core.base.insert_processing_infix(infix_str: str, filename: PathLike) → PathLike

Inserts an infix string into a filename before its extension.

Parameters:

• infix_str (str) – String to insert.

• filename (PathLike[AnyStr]) – Original filename.

Returns:

Modified filename with infix inserted.

Return type:

PathLike

src.core.base.extract_archive(archive_filepath: PathLike) → PathLike

Extracts an archive file (zip, tar, gzip).

Parameters:

archive_filepath (PathLike[AnyStr]) – Path to archive file.

Returns:

List of extracted file names or extracted filename for gzip.

Return type:

PathLike

Raises:

• FileNotFoundError – If the archive file does not exist.

• IOError – If the archive format is unsupported or extraction fails.

src.core.base.get_platform() → str

Detects the current operating system platform.

Returns:

Platform name ( ‘linux’, ‘freebsd’, ‘aix’, ‘macos’, ‘windows’, ‘unknown’).

Return type:

str

src.core.base.get_unique_path(parent_dir: PathLike = '.') → Path

Produce a Path object with directory name based on timestamp.

src.core.sample_data_container module

This module defines a container class for storing sample-related data paths and identifiers.

It includes attributes for R1 and R2 file paths, sample identifiers, and processing log paths.

class src.core.sample_data_container.SampleDataContainer(r1_source: PathLike, r2_source: PathLike = None, sid: str = '1', processing_path: PathLike = None, processing_logpath: PathLike = None, target_regions: list[tuple[str, str]] = None, bam_filepath: PathLike | None = None, vcf_filepath: PathLike | None = None, report_path: PathLike = None)

Bases: object

A container class for storing sample-related data paths and identifiers.

r1_source

Path to the R1 file.

Type:

PathLike[AnyStr]

r2_source

Path to the R2 file (optional).

Type:

Optional[PathLike[AnyStr]]

sid

Patient identifier.

Type:

str

processing_path

Path for storing processing logs.

Type:

PathLike[AnyStr]

processing_logpath

Path to processing logs.

Type:

PathLike[AnyStr]

bam_filepath

Path to BAM file (optional).

Type:

Optional[PathLike[AnyStr]]

vcf_filepath

Path to VCF file (optional).

Type:

Optional[PathLike[AnyStr]]

report_path

Path to the report directory.

Type:

PathLike[AnyStr]

r1_source

r2_source

sid

processing_path

processing_logpath

report_path

target_regions

bam_filepath

vcf_filepath

parse_regions(configurator: Configurator, path: PathLike = None, logger: Logger = None)

Parses target regions from a SAM file and updates the object’s target_regions attribute.

This method reads a SAM file (defaulting to a path based on the object’s processing_path and sid) and extracts chromosome information from sequence headers (@SQ lines). It formats the chromosome identifiers into interval strings (e.g., ‘chr01-interval’) and generates corresponding region tuples using the provided configurator.

Parameters:

• configurator (Configurator) – An instance used to generate region tuples from interval strings.

• path (PathLike[AnyStr], optional) – Path to the SAM file. If None, a default path based on the object’s processing_path and sid is used.

• logger (logging.Logger, optional) – Logger for logging critical errors encountered during file processing.

Raises:

FileNotFoundError, PermissionError, IOError, OSError – If the file cannot be opened or read, an exception is raised after logging the error if a logger is provided.

Side Effects:

Updates the object’s target_regions attribute with a list of region tuples generated from parsed chromosome intervals.

src.core.sample_data_factory module

This module defines an interface for a sample data factory and a base class for sample data containers.

It provides a way to parse sample data from various sources, storing the information in a structured manner.

The ISampleDataFactory protocol defines the required method for parsing sample data, and SampleDataContainer provides a common structure for storing sample data paths and identifiers.

The module utilizes the logging module for logging operations.

class src.core.sample_data_factory.ISampleDataFactory(*args, **kwargs)

Bases: Protocol

Interface for a sample data factory.

Defines the method parse_sample_data to be implemented by concrete classes.

parse_sample_data(path: PathLike, sample_id: AnyStr) → SampleDataContainer

Parses sample data from the given path

for the specified sample ID.

Parameters:

• path (PathLike[AnyStr]) – Directory path containing sample files.

• sample_id (AnyStr) – Identifier for the sample.

Returns:

An instance containing parsed sample data.

Return type:

SampleDataContainer

_abc_impl = <_abc._abc_data object>

_is_protocol = True

class src.core.sample_data_factory.SampleDataFactory(logger: Logger = None, outpath: PathLike = None)

Bases: LoggerMixin, ISampleDataFactory

Concrete implementation of the ISampleDataFactory interface.

Uses logging for error reporting and parsing sample data from files.

_abc_impl = <_abc._abc_data object>

_is_protocol = False

parse_sample_data(path: PathLike, sample_id: AnyStr) → SampleDataContainer

Parses sample data files from a directory based on the sample ID.

Looks for files containing

the sample ID and ‘R1’ or ‘R2’ in their names.

Parameters:

• path (PathLike[AnyStr]) – Directory path containing sample files.

• sample_id (AnyStr) – Identifier for the sample.

Returns:

An instance with source paths for R1 and R2, or None if files are not found.

Return type:

SampleDataContainer

Module contents