checkQC.run_type_recognizer module

class checkQC.run_type_recognizer.HiSeq2500

Bases: checkQC.run_type_recognizer.IlluminaInstrument

static name()

Name of the instrument, e.g. ‘nova_seq’

Returns:name of instrument as string

static reagent_version(runtype_recognizer)

Find run mode (rapid or not) and reagent version used for this run

:return run mode (as specified in RunInfo.xml) and reagent version

joint as one string e.g. rapidhighoutput_v4 or rapidrun_v2

class checkQC.run_type_recognizer.HiSeqX

Bases: checkQC.run_type_recognizer.IlluminaInstrument

static name()

Name of the instrument, e.g. ‘nova_seq’

Returns:name of instrument as string

static reagent_version(runtype_recognizer)

Reagent version, e.g. v1 Can used the provided runtype_recognizer to determined the exact reagent version

Parameters:runtype_recognizer – A instance of RuntypeRecognizer Returns:reagent version as a string

class checkQC.run_type_recognizer.ISeq

Bases: checkQC.run_type_recognizer.IlluminaInstrument

static name()

Name of the instrument, e.g. ‘nova_seq’

Returns:name of instrument as string

static reagent_version(runtype_recognizer)

Reagent version, e.g. v1 Can used the provided runtype_recognizer to determined the exact reagent version

Parameters:runtype_recognizer – A instance of RuntypeRecognizer Returns:reagent version as a string

class checkQC.run_type_recognizer.IlluminaInstrument

Bases: object

Base class representing an Illumina instrument. The name and reagent_version needs to be implemented by the specific subclasses.

static name()

Name of the instrument, e.g. ‘nova_seq’

Returns:name of instrument as string

static reagent_version(runtype_recognizer)

Reagent version, e.g. v1 Can used the provided runtype_recognizer to determined the exact reagent version

Parameters:runtype_recognizer – A instance of RuntypeRecognizer Returns:reagent version as a string

class checkQC.run_type_recognizer.MiSeq

Bases: checkQC.run_type_recognizer.IlluminaInstrument

static name()

Name of the instrument, e.g. ‘nova_seq’

Returns:name of instrument as string

static reagent_version(runtype_recognizer)

Find the reagent kit version (and flowcell mode if applicable) for this run

Returns:reagent version in format v[reagent kit version] or [flowcell mode]_v[reagent kit version], e.g. v3 or nano_v2

class checkQC.run_type_recognizer.NovaSeq

Bases: checkQC.run_type_recognizer.IlluminaInstrument

static name()

Name of the instrument, e.g. ‘nova_seq’

Returns:name of instrument as string

static reagent_version(runtype_recognizer)

Reagent version, e.g. v1 Can used the provided runtype_recognizer to determined the exact reagent version

Parameters:runtype_recognizer – A instance of RuntypeRecognizer Returns:reagent version as a string

class checkQC.run_type_recognizer.NovaSeqXPlus

Bases: checkQC.run_type_recognizer.IlluminaInstrument

static name()

Name of the instrument, e.g. ‘nova_seq’

Returns:name of instrument as string

static reagent_version(runtype_recognizer)

Reagent version, e.g. v1 Can used the provided runtype_recognizer to determined the exact reagent version

Parameters:runtype_recognizer – A instance of RuntypeRecognizer Returns:reagent version as a string

class checkQC.run_type_recognizer.RunTypeRecognizer(runfolder, runfolder_reader=<checkQC.runfolder_reader.RunfolderReader object>)

Bases: object

RunTypeRecognizer will read files in the runfolder to determine information about the run, such as the instrument type, the read length, etc.

The runfolder needs to have a ‘RunInfo.xml’ and a ‘[R|r]unParameters.xml’ file.

instrument_and_reagent_version()

Get the instrument and reagent version associated with this runfolder.

Returns:the joined instrument and reagent version, e.g. ‘hiseq2500_rapidrun_v2’

instrument_type()

This will look in the RunInfo.xml and determine the run type, based on the mappings from instrument names to instrument types

Raises:InstrumentTypeUnknown Returns:the instrument type of the runfolder

read_length()

Gather information on the read length of the run.

Returns:The read length. If multiple reads delimited by “-”, e.g. 150-150.