Possible bug

[Smeds]

CARtool/CombRegionInfo.py

Lines 2 to 35 in 9bb6b23

	def CombineRegionInfo(listToCompress, regions):
	from collections import OrderedDict
	previous_region = []
	current_region = []
	combine_temp = []
	newList=[]
	index=-1 # Since we compare with the previous start at -1 instead of 0 to jump one step and start with the first element as a previous value
	# Since we will save the previous value on the current line iteration we need one extra made up value in both lists to make sure the last elment is saved
	regions.append('end.extra')
	listToCompress.append(['end.extra'])
	for line in regions:
	current_region = line.split('.')
	current_region = current_region[0]
	if not(previous_region ==[]):
	if previous_region == current_region:
	combine_temp += listToCompress[index]
	else:
	combine_temp += listToCompress[index]
	newList.append(combine_temp)
	combine_temp = []
	index+=1
	previous_region=current_region
	# Removes the added elements to the input lists
	regions.pop()
	listToCompress.pop()
	return newList

Will this not combine regions wrongly, if input regions aren't sorted. And how does this function differ from CombineRegionInfo in CombineRows_generator.py

def CombineRegionInfo(listToCompress, regions):
	import re


	current_region = []
	combine_temp = {}
	newList=[]
	index=0 # Since we compare with the previous start at -1 instead of 0 to jump one step and start with the first element as a previous value


	for line in regions:
		current_region = re.split('\.|,|_',line)
		if (current_region[0] == 'iSNP' or current_region[0] == 'iIndel' or current_region[0] == 'MSI'):
			current_region[0] = "-".join([current_region[0],current_region[1],current_region[2]])
			current_region[1] = "-".join([current_region[0],current_region[1],current_region[2]])
			current_region[2] = "-".join([current_region[0],current_region[1],current_region[2]])
		current_region = current_region[0]


		if current_region in combine_temp.keys():
			combine_temp[current_region]=combine_temp[current_region]+listToCompress[index]


		else:
			combine_temp[current_region]=listToCompress[index]
		index+=1


	newList = [v for v in combine_temp.values()]
	# region_name = [k for k in combine_temp.keys()]


	return newList