1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
|
from extract_contexts import base_models
def tsv2matrix(tsvname,base):
base_model = base_models(base,False)
signals,contexts = {bm:{} for bm in base_model.values()},{bm:{} for bm in base_model.values()}
with open(tsvname,'r') as infi:
for line in infi:
#ecoli1 c183b422-5dda-4a23-b732-309e8f7f331f 1794509 ATGCGMTCCAG 1.49,1.93166666667,-0.385,5.615,5.36,-0.945,15.7357504216 - m6A
context,sigs,strand,label = line.split('\t')[3:7]
label = label.strip()
twobase_model = base_model[context[int(len(context)/2):int(len(context)/2)+2]]
if label not in signals[twobase_model]:
signals[twobase_model][label] = []
contexts[twobase_model][label] = []
if len(sigs.split(',')) >= 6 and len([x for x in sigs.split(',') if x == "0"]) == 0:
signals[twobase_model][label].append([float(s) for s in sigs.split(',')])
contexts[twobase_model][label].append(context)
return signals, contexts
|
