VCF_Variant.py

__author__  = "Jan-Simon Baasner"
__email__   = "janbaas@cebitec.uni-bielefeld.de"


from enum import Enum, unique

class Variant:
	"""
	A simple storage class for a vcf variant.
	Contains all its information.
	"""
	def __init__ (self,
				  chromosome: str,
				  position: int,
				  ID: int, #from vcf-file
				  usefullID: int, #not from vcf-file (count variants)
				  reference: str,
				  alternate: str,
				  qual: str,
				  filter_: str,
				  info: str) :
		"""
		Initialization of all information.
		Contains all information from the vcf file and one new ID for variant handling.
		:param chromosome: Chromosome.
		:param position: Position.
		:param ID: VCF ID
		:param usefullID: A real ID in numbers, which is unique.
		:param reference: VCF REF
		:param alternate: VCF ALT
		:param qual: VCF QUAL
		:param filter_: VCF Filter
		:param info: VCF Info
		"""


		#Initialization of variables
		self.Chromosome = chromosome
		self.Position = position
		self.ID = ID
		self.UsefullID = usefullID
		self.Reference = reference
		self.Alternate = alternate
		self.Qual = qual
		self.Filter = filter_
		self.Info = info
		self.ListofTranscripts =[]
		self.SListofTranscripts = []


class Variant_NAVIP(Variant):

	def __init__(self, Variation: Variant):
		super().__init__(Variation.Chromosome, Variation.Position, Variation.ID, Variation.UsefullID,
						 Variation.Reference, Variation.Alternate, Variation.Qual, Variation.Filter, Variation.Info )
		navip_line = self.Info.split("|NAVIP_END|")[0].split("|")
		self.TranskriptID = navip_line[0]
		self.Strand_Direction = navip_line[1]
		self.Variant_Classification = navip_line[2]
		self.Shared_Eff_Keys = navip_line[3]
		self.Ref_Codon = navip_line[4].split(";")[0]
		self.Ref_in_Codon_Position = navip_line[4].split(";")[1]
		self.Ref_AA = navip_line[5]
		self.Ref_Codon_CDS_Position = navip_line[6]
		self.Alt_Codon = navip_line[7].split(";")[0]
		self.Alt_in_Codon_Position = navip_line[7].split(";")[1]
		self.Alt_AA = navip_line[8]
		self.Alt_Codon_CDS_Position = navip_line[9]


		#		0				1				2
		# TranscriptID|Strand_Direction|Variant_Classification1,Variant_Classification2,...|
		#		3				4.1			4.2						5		6				7.1				7.2
		# Shared_EffKey(s)|REF_Codon(s);Variant_Position_in_Codon|REF_AA|old_CDS_Position|ALT_Codon(s);Variant_Position_in_Codon|
		#	8			9			10			11
		# ALT_AA|new_CDS_Position|NAVIP_END|<old info field>

@unique
class VariantEnum (Enum):
	"""
	Contains a few enums for variant usage only.
	"""
	DEFAULT = -1 # nothing decided (for finding errors - default should not exist in the output)
	NO_RASTER_NOW = -2
	NO_StartOfOwnEffect = -3
	NO_EndOfOwnEffect = -4