checkQC.run_type_recognizer module

class checkQC.run_type_recognizer.HiSeq2500[source]

Bases: checkQC.run_type_recognizer.IlluminaInstrument

static name()[source]

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

Returns:name of instrument as string
static reagent_version(runtype_recognizer)[source]

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[source]

Bases: checkQC.run_type_recognizer.IlluminaInstrument

static name()[source]

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

Returns:name of instrument as string
static reagent_version(runtype_recognizer)[source]

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[source]

Bases: checkQC.run_type_recognizer.IlluminaInstrument

static name()[source]

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

Returns:name of instrument as string
static reagent_version(runtype_recognizer)[source]

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[source]

Bases: object

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

static create_instrument_instance(instrument_name)[source]

Get the instrument instance corresponding to the given instrument name

Parameters:instrument_name – name of instrument to get the implementing class for
Returns:a instance of the corresponding IlluminaInstrument
static get_subclasses()[source]

Get all subclasses which extends this class (which should be all supported Illumina instruments)

Returns:a list of IlluminaInstrument subclasses
static name()[source]

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

Returns:name of instrument as string
static reagent_version(runtype_recognizer)[source]

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[source]

Bases: checkQC.run_type_recognizer.IlluminaInstrument

static name()[source]

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

Returns:name of instrument as string
static reagent_version(runtype_recognizer)[source]

Find the reagent version used for this run, as MiSeqs can have multiple different reagent kit versions.

Returns:reagent version of format v[number] e.g. v3
class checkQC.run_type_recognizer.NovaSeq[source]

Bases: checkQC.run_type_recognizer.IlluminaInstrument

static name()[source]

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

Returns:name of instrument as string
static reagent_version(runtype_recognizer)[source]

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>)[source]

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()[source]

Get the instrument and reagent version associated with this runfolder.

Returns:the joined instrument and reagent version, e.g. ‘hiseq2500_rapidrun_v2’
instrument_type()[source]

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()[source]

Gather information on the read length of the run.

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