Source code for methylprep.models.probes

# Lib
from enum import Enum, unique


[docs]@unique class Channel(Enum): """ idat probes measure either a red or green fluorescence. This specifies which to return within idat.py: red_idat or green_idat.""" RED = 'Red' GREEN = 'Grn' def __str__(self): return self.value @property def is_green(self): return self == self.GREEN @property def is_red(self): return self == self.RED
[docs]@unique class ProbeAddress(Enum): """AddressA_ID and AddressB_ID are columns in the manifest csv that contain internal Illumina probe identifiers. Type II probes use AddressA_ID; Type I uses both, because there are two probes, two colors. probe intensities in .idat files are keyed to one of these ids, but processed data is always keyed to the IlmnID probe "names" -- so this is used in converting between IDs. It is used to define probe sets below in this probes.py""" A = 'A' B = 'B' @property def header_name(self): if self == self.A: return 'AddressA_ID' return 'AddressB_ID'
[docs]@unique class ProbeType(Enum): """ probes can either be type I or type II for CpG or Snp sequences. Control probes are used for background correction in different fluorescence ranges and staining efficiency. Type I probes record EITHER a red or a green value. Type II probes record both values together. NOOB uses the red fluorescence on a green probe and vice versa to calculate background fluorescence.""" ONE = 'I' TWO = 'II' SNP_ONE = 'SnpI' SNP_TWO = 'SnpII' CONTROL = 'Control' # I was separating out mouse probes EARLY, here, but found they need to be processed like all other probes, THEN removed in post-processing stage. #MOUSE_ONE = 'MouseI' #MOUSE_TWO = 'MouseII' def __str__(self): return self.value @staticmethod def from_manifest_values(name, infinium_type): """ this function determines which of four kinds of probe goes with this name, using either the Infinium_Design_Type (I or II) or the name (starts with 'rs') and decides 'Control' is non of the above.""" is_control = any([name.startswith('rs'), name.startswith('ctl'), name.startswith('neg'), name.startswith('BSC'), name.startswith('NON'), ]) is_snp = name.startswith('rs') #is_mouse = name.startswith('mu') or name.startswith('rp') if is_control and is_snp: if infinium_type == 'I': return ProbeType.SNP_ONE elif infinium_type == 'II': return ProbeType.SNP_TWO else: return ProbeType.CONTROL elif is_control: return ProbeType.CONTROL #elif is_mouse: # return ProbeType.MOUSE_ONE if infinium_type == 'I' else ProbeType.MOUSE_TWO elif infinium_type == 'I': return ProbeType.ONE elif infinium_type == 'II': return ProbeType.TWO elif infinium_type in ('IR','IG'): # mouse only -- these are type I probes but Bret's files label them this way return ProbeType.ONE return ProbeType.CONTROL
[docs]class Probe(): """ this doesn't appear to be instantiated anywhere in methylprep """ __slots__ = [ 'address', 'illumina_id', 'probe_type', ] def __init__(self, address, illumina_id, probe_type): self.address = address self.illumina_id = illumina_id self.probe_type = probe_type
[docs]class ProbeSubset(): """ used below in probes.py to define sub-sets of probes: foreground-(red|green|all), or (un)methylated probes """ __slots__ = [ 'data_channel', 'probe_address', 'probe_channel', 'probe_type', ] def __init__(self, data_channel, probe_address, probe_channel, probe_type): self.data_channel = data_channel self.probe_address = probe_address self.probe_channel = probe_channel self.probe_type = probe_type def __str__(self): return f'{self.probe_type}-{self.probe_channel}' @property def is_green(self): return self.data_channel.is_green @property def is_red(self): return self.data_channel.is_red @property def column_name(self): return self.probe_address.header_name
#def get_probe_details(self, manifest): # return manifest.get_probe_details( # probe_type=self.probe_type, # channel=self.probe_channel, # ) METHYLATED_SNP_PROBES = ( ProbeSubset( data_channel=Channel.GREEN, probe_address=ProbeAddress.A, probe_channel=None, probe_type=ProbeType.SNP_TWO, ), ProbeSubset( data_channel=Channel.GREEN, probe_address=ProbeAddress.B, probe_channel=Channel.GREEN, probe_type=ProbeType.SNP_ONE, ), ProbeSubset( data_channel=Channel.RED, probe_address=ProbeAddress.B, probe_channel=Channel.RED, probe_type=ProbeType.SNP_ONE, ), ) UNMETHYLATED_SNP_PROBES = ( ProbeSubset( data_channel=Channel.RED, probe_address=ProbeAddress.A, probe_channel=None, probe_type=ProbeType.SNP_TWO, ), ProbeSubset( data_channel=Channel.GREEN, probe_address=ProbeAddress.A, probe_channel=Channel.GREEN, probe_type=ProbeType.SNP_ONE, ), ProbeSubset( data_channel=Channel.RED, probe_address=ProbeAddress.A, probe_channel=Channel.RED, probe_type=ProbeType.SNP_ONE, ), ) FG_GREEN_PROBE_SUBSETS = ( ProbeSubset( data_channel=Channel.GREEN, probe_address=ProbeAddress.A, probe_channel=None, probe_type=ProbeType.TWO, ), ProbeSubset( data_channel=Channel.GREEN, probe_address=ProbeAddress.A, probe_channel=Channel.GREEN, probe_type=ProbeType.ONE, ), ProbeSubset( data_channel=Channel.GREEN, probe_address=ProbeAddress.B, probe_channel=Channel.GREEN, probe_type=ProbeType.ONE, ), ) FG_RED_PROBE_SUBSETS = ( ProbeSubset( data_channel=Channel.RED, probe_address=ProbeAddress.A, probe_channel=None, probe_type=ProbeType.TWO, ), ProbeSubset( data_channel=Channel.RED, probe_address=ProbeAddress.A, probe_channel=Channel.RED, probe_type=ProbeType.ONE, ), ProbeSubset( data_channel=Channel.RED, probe_address=ProbeAddress.B, probe_channel=Channel.RED, probe_type=ProbeType.ONE, ), ) FG_PROBE_SUBSETS = { Channel.GREEN: FG_GREEN_PROBE_SUBSETS, Channel.RED: FG_RED_PROBE_SUBSETS, } METHYLATED_PROBE_SUBSETS = ( # == IG[AddressB] + II[green] + IR[AddressB] ProbeSubset( data_channel=Channel.GREEN, probe_address=ProbeAddress.A, probe_channel=None, probe_type=ProbeType.TWO, ), ProbeSubset( data_channel=Channel.GREEN, probe_address=ProbeAddress.B, probe_channel=Channel.GREEN, probe_type=ProbeType.ONE, ), ProbeSubset( data_channel=Channel.RED, probe_address=ProbeAddress.B, probe_channel=Channel.RED, probe_type=ProbeType.ONE, ), ) UNMETHYLATED_PROBE_SUBSETS = ( # == IG [AddressA] + II[red] + IR[AddressA] ProbeSubset( data_channel=Channel.RED, probe_address=ProbeAddress.A, probe_channel=None, probe_type=ProbeType.TWO, ), ProbeSubset( data_channel=Channel.GREEN, probe_address=ProbeAddress.A, probe_channel=Channel.GREEN, probe_type=ProbeType.ONE, ), ProbeSubset( data_channel=Channel.RED, probe_address=ProbeAddress.A, probe_channel=Channel.RED, probe_type=ProbeType.ONE, ), ) ''' DISABLED because these faster to process with normals then remove during postprocessing. METHYLATED_MOUSE_PROBES = ( ProbeSubset( data_channel=Channel.GREEN, probe_address=ProbeAddress.A, probe_channel=None, probe_type=ProbeType.MOUSE_TWO, ), ProbeSubset( data_channel=Channel.GREEN, probe_address=ProbeAddress.B, probe_channel=Channel.GREEN, probe_type=ProbeType.MOUSE_ONE, ), ProbeSubset( data_channel=Channel.RED, probe_address=ProbeAddress.B, probe_channel=Channel.RED, probe_type=ProbeType.MOUSE_ONE, ), ) UNMETHYLATED_MOUSE_PROBES = ( ProbeSubset( data_channel=Channel.RED, probe_address=ProbeAddress.A, probe_channel=None, probe_type=ProbeType.MOUSE_TWO, ), ProbeSubset( data_channel=Channel.GREEN, probe_address=ProbeAddress.A, probe_channel=Channel.GREEN, probe_type=ProbeType.MOUSE_ONE, ), ProbeSubset( data_channel=Channel.RED, probe_address=ProbeAddress.A, probe_channel=Channel.RED, probe_type=ProbeType.MOUSE_ONE, ), ) # SNP-PREP-NOTES from JAN 2020 # notebook equivalent of SNP_PROBES below. #manifest = data_containers[0].manifest.data_frame #snpProbesI = manifest[manifest['probe_type']=='SnpI'] #snpProbesI_Grn = snpProbesI[snpProbesI['Color_Channel']=='Grn'] #snpProbesI_Red = snpProbesI[snpProbesI['Color_Channel']=='Red'] #snpProbesII = manifest[manifest['probe_type']=='SnpII'] SNP_PROBES = ( # SNP_II_PROBES ProbeSubset( data_channel=Channel.GREEN, probe_address=ProbeAddress.A, probe_channel=None, probe_type=ProbeType.SNP_TWO, ), # SNP_I_GREEN_PROBES ProbeSubset( data_channel=Channel.GREEN, probe_address=ProbeAddress.A, probe_channel=Channel.GREEN, probe_type=ProbeType.SNP_ONE, ), # SNP_I_RED_PROBES ProbeSubset( data_channel=Channel.RED, probe_address=ProbeAddress.B, probe_channel=Channel.RED, probe_type=ProbeType.SNP_ONE, ) ) '''