Python字典，使每一個奇數行向密鑰和偶數行從文件

Question

喜價值，我有一個文本文件中像這樣：

>NM_145914.2:212 
TCTGATGGTAAAAGTCGAGGAGAAAGAAGA 
>NM_000614.3:1086 
ATTCAATTTAAAATCAGACTCTTTAGTTGA 
>NM_012096.2:2808 
CAGTTAAGGTTTCAAATTGTGGCAGGTGGT 
>NM_173465.3:1682 
GTGCGTCGGGTGAGAGAGGCCCCAGCGGCC 
>NM_001198858.1:490 
CAACCACCACAACCTGCTGGTCTGCTCGGT 
......more lines in same style...... 

我要的是：

從上面的文件中讀取，使行1,3,5,7 ...到字典鍵和行2,4,5,8 ...到字典值。

我的代碼是：

query_dict = {} 
nameAt = 1 
sequenceAt = 2 

while name in range(totalLines): 
line1 = linecache.getline(filename, nameAt) 
line2 = linecache.getline(filename, sequenceAt) 

query_dict[line1] = line2 
nameAt = nameAt + 2   
sequenceAt = sequenceAt + 2 

代碼的工作，但它的速度很慢，因爲我的文本文件的最低線爲20萬線。有沒有人有更好的方法來做到這一點？

非常感謝。

==============添加後續問題==================

這裏是FASTQ格式，與每個讀取（記錄）4行：

@>NM_052972.2:11:1054:1780:889 
CTTCGACATCTCCGGCAACCCCTGGATCTG 
+>NM_052972.2:11:1054:1780:889 
IIIIIIIIIIIIIIIIIIIIIIIIIIIIII 
@>NM_080660.3:12:914:1802:542 
CCTGTATGGCTACTGCAACCTCAAGGATAA 
+>NM_080660.3:12:914:1802:542 
IIIIIIIIIIIIIIIIIIIIIIIIIIIIII 
@>NM_176814.3:712:2706:4242:98 
ACAGAGTAAAAGAGAGGCTGACTTAATAAA 
+>NM_176814.3:712:2706:4242:98 
IIIIIIIIIIIIIIIIIIIIIIIIIIIIII 
...... more lines in same style ...... 

我想創建一個字典，關鍵是第一線和所述值在各4行記錄的第二線。

字典會是什麼樣子：

{'@>NM_052972.2:11:1054:1780:889':'CTTCGACATCTCCGGCAACCCCTGGATCTG', 
'@>NM_080660.3:12:914:1802:542':'CCTGTATGGCTACTGCAACCTCAAGGATAA', 
'@>NM_176814.3:712:2706:4242:98':'ACAGAGTAAAAGAGAGGCTGACTTAATAAA', 
..... more keys and values ...... 
} 

感謝。

Answer 1

事情是這樣的：

with open('filename') as f: 
    query_dict = {line.strip():next(f).strip() for line in f} 

輸出：

>>> from pprint import pprint 
>>> pprint(query_dict) 
{'>NM_000614.3:1086': 'ATTCAATTTAAAATCAGACTCTTTAGTTGA', 
'>NM_001198858.1:490': 'CAACCACCACAACCTGCTGGTCTGCTCGGT', 
'>NM_012096.2:2808': 'CAGTTAAGGTTTCAAATTGTGGCAGGTGGT', 
'>NM_145914.2:212': 'TCTGATGGTAAAAGTCGAGGAGAAAGAAGA', 
'>NM_173465.3:1682': 'GTGCGTCGGGTGAGAGAGGCCCCAGCGGCC'} 

更新：

with open('foo.txt') as f: 
    dic = {} 
    for line in f: 
     dic[line.strip()] = next(f).strip() 
     next(f);next(f) #Drop next two lines 
from pprint import pprint 
pprint(dic) 

輸出：

{'@>NM_052972.2:11:1054:1780:889': 'CTTCGACATCTCCGGCAACCCCTGGATCTG', 
'@>NM_080660.3:12:914:1802:542': 'CCTGTATGGCTACTGCAACCTCAAGGATAA', 
'@>NM_176814.3:712:2706:4242:98': 'ACAGAGTAAAAGAGAGGCTGACTTAATAAA'} 

Answer 2

>>> s = """>NM_145914.2:212 
... TCTGATGGTAAAAGTCGAGGAGAAAGAAGA 
... >NM_000614.3:1086 
... ATTCAATTTAAAATCAGACTCTTTAGTTGA 
... >NM_012096.2:2808 
... CAGTTAAGGTTTCAAATTGTGGCAGGTGGT 
... >NM_173465.3:1682 
... GTGCGTCGGGTGAGAGAGGCCCCAGCGGCC 
... >NM_001198858.1:490 
... CAACCACCACAACCTGCTGGTCTGCTCGGT""".splitlines() 
>>> {i: j for i, j in zip(s[::2], s[1::2])} 
{'>NM_145914.2:212': 'TCTGATGGTAAAAGTCGAGGAGAAAGAAGA', '>NM_000614.3:1086': 'ATTCAATTTAAAATCAGACTCTTTAGTTGA', '>NM_001198858.1:490': 'CAACCACCACAACCTGCTGGTCTGCTCGGT', '>NM_012096.2:2808': 'CAGTTAAGGTTTCAAATTGTGGCAGGTGGT', '>NM_173465.3:1682': 'GTGCGTCGGGTGAGAGAGGCCCCAGCGGCC'} 

使用itertools.islice如果記憶是一個問題：

{i: j for i, j in zip(islice(s, 0, len(s), 2), islice(s, 1, len(s), 2))} 

Answer 3

或者，而不是一個字典-COMP：

from itertools import izip 

with open('somefile') as fin: 
    lines = (line.strip() for line in fin) 
    query_dict = dict(izip(lines, lines)) 

Answer 4

這是一個FASTA文件。安裝Biopython（pip install biopython），並對其進行解析：

from Bio import SeqIO 

with open('filename.fasta', 'rU') as handle: 
    for record in SeqIO.parse(handle, 'fasta'): 
     print(record) 

看那條可讀的輸出：

ID: NM_145914.2:212 
Name: NM_145914.2:212 
Description: NM_145914.2:212 
Number of features: 0 
Seq('TCTGATGGTAAAAGTCGAGGAGAAAGAAGA', SingleLetterAlphabet()) 
...