Review APARENT predictions

[Hoeze]

Currently, the APARENT dataloader gets the PolyA sites from the transcript GTF annotation:

models/APARENT/veff/dataloader.py

Lines 87 to 111 in ae8cf12

	def get_roi_from_transcript(transcript_start: int, transcript_end: int, is_on_negative_strand: bool) -> (int, int):
	"""
	Get region-of-interest for APARENT in relation to the 3'UTR of a transcript
	:param transcript_start: 0-based start position of the transcript
	:param transcript_end: 1-based end position of the transcript
	:param is_on_negative_strand: is the gene on the negative strand?
	:return: Tuple of (start, end) position for the region of interest
	"""
	# CSE should be roughly around position 70 of the 205bp sequence.
	# Since CSE is likely 30bp upstream of the cut site, we shift the cut site
	# by 100bp upstream and 105bp downstream
	if is_on_negative_strand:
	end = transcript_start + 100
	# convert 0-based to 1-based
	end += 1
	start = end - 205
	else:
	start = transcript_end - 100
	# convert 1-based to 0-based
	start -= 1
	end = start + 205
	return start, end

@johli Is this a viable implementation of the strategy you explained here?
Do you maybe have some example data (vcf file + scores) against which we could compare the Kipoi predictions?

xref: #342
xref: johli/aparent#8