[英]Python Storing & Printing Data from a text file
我正在尝试一个Python脚本,该脚本从用户那里获取某些字母的序列(A,C,G和T),并打印A,C,G和T的百分比。
例如,如果用户键入AGGTGACCCT,则输出应为A:20 C:30 G:30 T:20
我对Java有相当的经验,但是对Python还是陌生的。 我没有像在Java中那样使用扫描仪。 我尝试搜索参考库,但无法真正找出任何答案。
collections.Counter是一个非常方便的工具,值得您开始使用python学习。
from collections import Counter
inp = input("Enter letters") # input() if using python 3
l = len(inp.strip()) # get length of input string ,inp.strip() removes any whitespace, just use len(inp) if you want to include
c = Counter(inp)
for char in c:
c[char] = c[char] * 100 / l # don't need to cast as float for python 3
print (c)
Counter({'C': 30.0, 'G': 30.0, 'A': 20.0, 'T': 20.0})
有一个具有DictWriter的模块csv
,该DictWriter能够将数据写入文件。
您可以直接从标准输入流sys.stdin
,如下所示:
$ cat read.py
import sys
userin = sys.stdin.read()
print [c for c in userin]
$ python read.py
HELLO
['H', 'E', 'L', 'L', 'O', '\n']
然后,您可以将文本文件通过管道传递到stdin,例如:
$ cat input.txt
HELLO
$ python read.py < input.txt
['H', 'E', 'L', 'L', 'O', '\n']
或者,如果您想直接读取文件:
>>> import io
>>> with io.open('input.txt', mode='rb') as f:
... print [c for c in f.read()]
...
['H', 'E', 'L', 'L', 'O', '\n']
如果您可以将序列保存在以逗号分隔的文件(csv)中,则可以执行以下操作:
import pandas as pd
sequence = pd.read_csv(file_name)
As = 0
Cs = 0
Gs = 0
Ts = 0
total = len(sequence)
for letter in sequence:
if letter == 'A':
As += 1.0
elif letter == 'C':
Cs += 1.0
elif letter == 'G':
Gs += 1.0
elif letter == 'T':
Ts += 1.0
percent_A = As/total
percent_C = As/total
percent_T = As/total
percent_G = As/total
要么:
import pandas as pd
sequence_list = []
sequence = pd.read_csv(file_name)
for letter in sequence:
sequence_list.append(letter)
As = sequence_list.count('A')
Cs = sequence_list.count('C')
Gs = sequence_list.count('G')
Ts = sequence_list.count('T')
total = len(sequence_list)
percent_A = As/total
percent_C = As/total
percent_T = As/total
percent_G = As/total
这种通用结构也适用于tsv。
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