我有一个带有染色体坐标的字典，如以下示例所示：
==我想创建一个字典列表，其中那些具有最小和最大染色体坐标（字典值）的当前键与至少可以重叠的1000个键重叠在一起，然后归为一本新词典是新列表中的单独词典。
所以理想的情况是：
First_dict = {Key1: ['chr10', 19010495, 19014590, 19014064],
Key2: ['chr10', 19010495, 19014658],
Key3: ['chr10', 19010502, 19014641],
Key4: ['chr10', 37375766, 37377526],
Key5: ['chr10', 76310389, 76315990, 76312224, 76312963],
Key6: ['chr11', 14806147, 14814006]}
其中key1，key2和key3由于它们的染色体坐标重叠而在New_list中组合在一起作为新字典，而key4，key5，key6是与New_list的单独词典，因为它们根本不重叠。
我最初的想法是使用“
”将“ First_dict”分隔成词典列表New_list =
[{Key1: ['chr10', 19010495, 19014590, 19014064],Key2: ['chr10', 19010495, 19014658], Key3: ['chr10', 19010502, 19014641]},
{Key4: ['chr10', 37375766, 37377526]},
{Key5: ['chr10', 76310389, 76315990, 76312224, 76312963]},
{Key6: ['chr11', 14806147, 14814006]}]
，然后遍历每个字典以将最小值和最大值与上一个字典进行比较，以检查是否重叠，然后创建一个新列表。但是我有几个问题，我无法解决。
我也在寻找将字典归类的其他问题，例如在问题中： Grouping Python dictionary keys as a list and create a new dictionary with this list as a value
但是我的问题是，如上例所示，我的价位并不总是完全相同。在考虑重叠时，我还必须考虑染色体。
有人可以帮助解决这个问题吗？还是可以提出建议？非常感谢。
答案 0 :(得分：1)
这个问题可能更适合基于图形的解决方案。没有什么可以防止多个范围以不同的时间间隔重叠。
#!/usr/bin/env python3
from pprint import pprint
from itertools import groupby
def mapper(d, overlap=1000):
"""Each chromsomal coordinate must be interrogated
to determine if it is within +/-overlap of any other
Range within any other Original Dictionary Transcript
value will match key and chromosome element from the list
------------------------ ---------------------- ----------
(el-overlap, el+overlap), (dict-key, chromosome), el)
"""
for key, ch in d.items():
for el in ch[1:]:
yield ((el-overlap, el+overlap), (key, ch[0]), el)
def sorted_mapper(d, overlap=1000):
"""Simply sort the mapper data by its first element
"""
for r in sorted(mapper(d, overlap), key=lambda x: x[0]):
yield r
def groups(iter_):
previous = next(iter_)
retval = [previous]
for chrm in iter_:
if previous[0][0] <= chrm[-1] <= previous[0][1]:
retval.append(chrm)
else:
yield retval
previous = chrm
retval = [previous]
yield retval
def reduce_phase1(iter_):
for l in iter_:
retval = {}
for (minc, maxc), (key, lbl), chrm in l:
x = retval.get(key,[lbl])
x.append(chrm)
retval[key] = x
yield retval
def update_dict(d1, d2):
retval = d1
for key, value in d2.items():
if key in d1.keys():
retval[key].extend(value[1:])
return retval
def reduce_phase2(iter_):
retval = [next(iter_)]
retval_keys = [set([k for k in retval[0].keys()])]
for d in iter_:
keyset = set([k for k in d.keys()])
isnew = True
for i, e in enumerate(retval_keys):
if keyset <= e:
isnew = False
retval[i] = update_dict(retval[i], d)
if isnew:
retval.append(d)
retval_keys.append(keyset)
return retval
First_dict = {Key1: ['chr10', 19010495, 19014590, 19014064],
Key2: ['chr10', 19010495, 19014658],
Key3: ['chr10', 19010502, 19014641],
Key4: ['chr10', 37375766, 37377526],
Key5: ['chr10', 76310389, 76315990, 76312224, 76312963],
Key6: ['chr11', 14806147, 14814006]}
New_list = [
{
"Key1": ['chr10', 19010495, 19014590, 19014064],
"Key2": ['chr10', 19010495, 19014658],
"Key3": ['chr10', 19010502, 19014641]
},
{"Key4": ['chr10', 37375766, 37377526]},
{"Key5": ['chr10', 76310389, 76315990, 76312224, 76312963]},
{"Key6": ['chr11', 14806147, 14814006]}
]
pprint(First_dict)
print('-'*40)
g = groups(sorted_ranges(First_dict))
p1 = reduce_phase1(groups(sorted_ranges(First_dict)))
p2 = reduce_phase2(p1)
pprint(p2)
{'Key1': ['chr10', 19010495, 19014590, 19014064],
'Key2': ['chr10', 19010495, 19014658],
'Key3': ['chr10', 19010502, 19014641],
'Key4': ['chr10', 37375766, 37377526],
'Key5': ['chr10', 76310389, 76315990, 76312224, 76312963],
'Key6': ['chr11', 14806147, 14814006]}
----------------------------------------
[{'Key6': ['chr11', 14806147, 14814006]},
{'Key1': ['chr10', 19010495, 19014064, 19014590],
'Key2': ['chr10', 19010495, 19014658],
'Key3': ['chr10', 19010502, 19014641]},
{'Key4': ['chr10', 37375766, 37377526]},
{'Key5': ['chr10', 76310389, 76312224, 76312963, 76315990]}]
映射器为每个字典键和染色体元素发出一条记录。每个记录都有一个关联范围，可以在其中匹配其元素。
((el-1000, el+1000), (dict-key, chromosome), el)
（el-1000，el + 1000）是任何其他染色体元素都可以匹配的范围。
（字典键，染色体）该染色体的原始字典。
el 是染色体坐标中的一个元素。
((19009495, 19011495), ('Key1', 'chr10'), 19010495)
((19013590, 19015590), ('Key1', 'chr10'), 19014590)
((19013064, 19015064), ('Key1', 'chr10'), 19014064)
((19009495, 19011495), ('Key2', 'chr10'), 19010495)
((19013658, 19015658), ('Key2', 'chr10'), 19014658)
((19009502, 19011502), ('Key3', 'chr10'), 19010502)
((19013641, 19015641), ('Key3', 'chr10'), 19014641)
((37374766, 37376766), ('Key4', 'chr10'), 37375766)
((37376526, 37378526), ('Key4', 'chr10'), 37377526)
((76309389, 76311389), ('Key5', 'chr10'), 76310389)
((76314990, 76316990), ('Key5', 'chr10'), 76315990)
((76311224, 76313224), ('Key5', 'chr10'), 76312224)
((76311963, 76313963), ('Key5', 'chr10'), 76312963)
((14805147, 14807147), ('Key6', 'chr11'), 14806147)
((14813006, 14815006), ('Key6', 'chr11'), 14814006)
注意：：映射器的输出未排序。
我们需要使用（el-1000，el + 1000）作为键对转换后的数据进行排序。
这将使我们检查下一个值是否在上一个值的范围内。由于键是按排序顺序排列的，因此我们可以将指定重叠范围内的值链接在一起。
((14805147, 14807147), ('Key6', 'chr11'), 14806147)
((14813006, 14815006), ('Key6', 'chr11'), 14814006)
((19009495, 19011495), ('Key1', 'chr10'), 19010495)
((19009495, 19011495), ('Key2', 'chr10'), 19010495)
((19009502, 19011502), ('Key3', 'chr10'), 19010502)
((19013064, 19015064), ('Key1', 'chr10'), 19014064)
((19013590, 19015590), ('Key1', 'chr10'), 19014590)
((19013641, 19015641), ('Key3', 'chr10'), 19014641)
((19013658, 19015658), ('Key2', 'chr10'), 19014658)
((37374766, 37376766), ('Key4', 'chr10'), 37375766)
((37376526, 37378526), ('Key4', 'chr10'), 37377526)
((76309389, 76311389), ('Key5', 'chr10'), 76310389)
((76311224, 76313224), ('Key5', 'chr10'), 76312224)
((76311963, 76313963), ('Key5', 'chr10'), 76312963)
((76314990, 76316990), ('Key5', 'chr10'), 76315990)
对指定重叠范围内的值进行分组。 出现的列表将包含来自染色体的值 在先前染色体的重叠范围内。
[((14805147, 14807147), ('Key6', 'chr11'), 14806147)]
----------------------------------------
[((14813006, 14815006), ('Key6', 'chr11'), 14814006)]
----------------------------------------
[((19009495, 19011495), ('Key1', 'chr10'), 19010495),
((19009495, 19011495), ('Key2', 'chr10'), 19010495),
((19009502, 19011502), ('Key3', 'chr10'), 19010502)]
----------------------------------------
[((19013064, 19015064), ('Key1', 'chr10'), 19014064),
((19013590, 19015590), ('Key1', 'chr10'), 19014590),
((19013641, 19015641), ('Key3', 'chr10'), 19014641),
((19013658, 19015658), ('Key2', 'chr10'), 19014658)]
----------------------------------------
[((37374766, 37376766), ('Key4', 'chr10'), 37375766)]
----------------------------------------
[((37376526, 37378526), ('Key4', 'chr10'), 37377526)]
----------------------------------------
[((76309389, 76311389), ('Key5', 'chr10'), 76310389)]
----------------------------------------
[((76311224, 76313224), ('Key5', 'chr10'), 76312224),
((76311963, 76313963), ('Key5', 'chr10'), 76312963)]
----------------------------------------
[((76314990, 76316990), ('Key5', 'chr10'), 76315990)]
----------------------------------------
通过删除工程功能来清理数据。
{'Key6': ['chr11', 14806147]}
----------------------------------------
{'Key6': ['chr11', 14814006]}
----------------------------------------
{'Key1': ['chr10', 19010495],
'Key2': ['chr10', 19010495],
'Key3': ['chr10', 19010502]}
----------------------------------------
{'Key1': ['chr10', 19014064, 19014590],
'Key2': ['chr10', 19014658],
'Key3': ['chr10', 19014641]}
----------------------------------------
{'Key4': ['chr10', 37375766]}
----------------------------------------
{'Key4': ['chr10', 37377526]}
----------------------------------------
{'Key5': ['chr10', 76310389]}
----------------------------------------
{'Key5': ['chr10', 76312224, 76312963]}
----------------------------------------
{'Key5': ['chr10', 76315990]}
----------------------------------------
将置换的字典键与其键合在一起 原始字典。附加相应的值 字典键匹配时的染色体。
{'Key6': ['chr11', 14806147, 14814006]}
----------------------------------------
{'Key1': ['chr10', 19010495, 19014064, 19014590],
'Key2': ['chr10', 19010495, 19014658],
'Key3': ['chr10', 19010502, 19014641]}
----------------------------------------
{'Key4': ['chr10', 37375766, 37377526]}
----------------------------------------
{'Key5': ['chr10', 76310389, 76312224, 76312963, 76315990]}
----------------------------------------