I'm not an expert in Python so forgive me if I'm wrong, but I've tried to decompose the Call.py function to understand how the counttables used in the DESeq analysis are generated.
Within the create_subfamily_dict function, the count assigned into the dictionary is the uniq_counts rather than the total counts used elsewhere:
def create_subfamily_dict(infilepath,count_dict):
TE_classes=["LTR","LINE","SINE","Retroposon","DNA","RC"]
with open(infilepath,'r') as infile:
for line in infile:
line = line.rstrip()
line = line.split("\t")
taxo = line[2]
count=line[6]
if any(x in taxo for x in TE_classes):
if count=="tot_counts":
continue
else:
count = str(int(round(float(line[5]))))
sample = line[0]
if taxo not in count_dict:
count_dict[taxo] = {sample:count}
else:
count_dict[taxo][sample]=count
I'm not an expert in Python so forgive me if I'm wrong, but I've tried to decompose the Call.py function to understand how the counttables used in the DESeq analysis are generated.
Within the create_subfamily_dict function, the count assigned into the dictionary is the uniq_counts rather than the total counts used elsewhere:
def create_subfamily_dict(infilepath,count_dict): TE_classes=["LTR","LINE","SINE","Retroposon","DNA","RC"] with open(infilepath,'r') as infile: for line in infile: line = line.rstrip() line = line.split("\t") taxo = line[2] count=line[6]
if any(x in taxo for x in TE_classes):
if count=="tot_counts": continue else: count = str(int(round(float(line[5])))) sample = line[0] if taxo not in count_dict: count_dict[taxo] = {sample:count} else:
count_dict[taxo][sample]=count
Can you explain why this is the case?