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[英]creating a table from a txt file of nested dictionaries within a list using python
[英]Creating multiple nested dictionaries from .txt file
我正在尝试创建由多个词典组成的字典。 我是从.txt文件创建此文件的:
chrY 6 8 +
chrY 3 5 +
chrX 10 11 +
chrX 13 15 -
我想要的输出将是:
{'chrY': {'+' : {'start': [3 , 6], 'end': [5, 8]}}, 'chrX': {'+' : {'start': [10], 'end': [11]} , '-': {'start' : [13], 'end' : [15]}}}
到目前为止,我的代码包括:
import sys
first_dict = {}
intron_dict = {}
def main():
with open(sys.argv[1], 'r') as intron:
for line in intron.readlines():
line = line.split()
chromosome = line[0]
start = line[1]
end = line[2]
strand = line[3]
first_dict = {chromosome : (strand, start, end)}
for k, v in first_dict.iteritems():
intron_dict.setdefault(k, []).append(v)
print (intron_dict)
if __name__=='__main__':
main()
此代码使我可以对chrY和chrX键进行排序,而不会覆盖值。 我在合并“ +”和“-”键并将数据转换为所需格式时遇到问题。 到目前为止,我的输出看起来像:
{'chrY': [('+', '6', '8'), ('+', '3', '5')], 'chrX': [('+', '10', '11'), ('-', '13', '15')]}
您可以使用嵌套的defaultdict
来简化代码,其中第三级的值是列表:
from collections import defaultdict
result = defaultdict(lambda: defaultdict(lambda: defaultdict(list)))
with open('test.txt') as f:
for row in f:
ch, start, end, op = row.split()
result[ch][op]['start'].append(start)
result[ch][op]['end'].append(end)
import json
print(json.dumps(result, indent=4))
输出:
{
"chrY": {
"+": {
"start": [
"6",
"3"
],
"end": [
"8",
"5"
]
}
},
"chrX": {
"+": {
"start": [
"10"
],
"end": [
"11"
]
},
"-": {
"start": [
"13"
],
"end": [
"15"
]
}
}
}
一种方法是使用defaultdict。 例如:
import sys
from pprint import pprint
from collections import defaultdict
first_dict = defaultdict(dict)
intron_dict = {}
d = dict()
def main():
with open('test.csv', 'r') as intron:
for line in intron.readlines():
chromosome, start, end, strand, = line.split()
if strand not in first_dict[chromosome]:
first_dict[chromosome][strand] = defaultdict(list)
first_dict[chromosome][strand]['start'].append(start)
first_dict[chromosome][strand]['end'].append(end)
pprint(first_dict)
if __name__=='__main__':
main()
结果是:
defaultdict(<class 'dict'>,
{'chrX': {'+': defaultdict(<class 'list'>,
{'end': ['11'],
'start': ['10']}),
'-': defaultdict(<class 'list'>,
{'end': ['15'],
'start': ['13']})},
'chrY': {'+': defaultdict(<class 'list'>,
{'end': ['8', '5'],
'start': ['6', '3']})}})
这是另一种没有defaultdict
方法。 只是使用if ... else
import sys
intron_dict = dict()
def main():
with open(sys.argv[1], 'r') as intron:
for line in intron.readlines():
line = line.split()
chromosome = line[0]
start = int(line[1]) # converted to int to avoid quotes in result
end = int(line[2])
strand = line[3]
first_dict = {strand : {'start' : [start], 'end' : [end]}}
if intron_dict.has_key(chromosome):
if intron_dict[chromosome].has_key(strand):
intron_dict[chromosome][strand]['start'].append(start)
intron_dict[chromosome][strand]['end'].append(end)
else:
intron_dict[chromosome][strand] = first_dict[strand]
else:
intron_dict.setdefault(chromosome, first_dict)
print (intron_dict)
if __name__=='__main__':
main()
输出:
{'chrY': {'+': {'start': [6, 3], 'end': [8, 5]}}, 'chrX': {'+': {'start': [10], 'end': [11]}, '-': {'start': [13], 'end': [15]}}}
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