小编Xio*_*g89的帖子

我想为一组DNA序列生成一个热编码.例如,序列ACGTCCA可以以转置方式如下表示.但是下面的代码将以水平方式生成一个热编码,我希望它以垂直形式.谁能帮我？

ACGTCCA 
1000001 - A
0100110 - C 
0010000 - G
0001000 - T

示例代码:

from sklearn.preprocessing import OneHotEncoder
import itertools

# two example sequences
seqs = ["ACGTCCA","CGGATTG"]


# split sequences to tokens
tokens_seqs = [seq.split("\\") for seq in seqs]

# convert list of of token-lists to one flat list of tokens
# and then create a dictionary that maps word to id of word,
# like {A: 1, B: 2} here
all_tokens = itertools.chain.from_iterable(tokens_seqs)
word_to_id = {token: idx for …

我想将下面的值标准化为水平而不是垂直。代码读取代码后提供的csv文件，并输出具有标准化值的新csv文件。如何使其水平标准化？给出如下代码：

码

#norm_code.py
#normalization = x-min/max-min

import numpy as np
from sklearn import preprocessing
all_data=np.loadtxt(open("c:/Python27/test.csv","r"),
delimiter=",",
skiprows=0,
dtype=np.float64)

x=all_data[:]

print('total number of samples (rows):', x.shape[0])
print('total number of features (columns):', x.shape[1])
minmax_scale = preprocessing.MinMaxScaler(feature_range=(0, 1)).fit(x)

X_minmax=minmax_scale.transform(x)
with open('test_norm.csv',"w") as f:
    f.write("\n".join(",".join(map(str, x)) for x in (X_minmax)))

test.csv

1   2   0   4   3
3   2   1   1   0
2   1   1   0   1

我想在两个列表中划分列表项.

a = [[1, 0, 2], [0, 0, 0], [1], [1]]
b = [[5, 6, 4], [6, 6, 6], [3], [3]]

如何将a除以b来获得此输出:

c = [[0.2, 0, 0.5], [0, 0, 0], [0.333], [0.333]]

谁能帮我？

我有一些字符串,我想删除每个字符串的最后一个字符.当我尝试下面的代码时,它会删除我的第二行字符串,而不是删除最后一个元素.以下是我的代码:

码

with open('test.txt') as file:
    seqs=file.read().splitlines()
    seqs=seqs[:-1]

的test.txt

ABCABC
XYZXYZ

产量

ABCABC

期望的输出

ABCAB
XYZXY

如何计算具有少量数组的列表中某个整数的出现？例如,我想查找值2的出现次数.

import numpy as np
a = [np.array([2, 2, 1, 2]), np.array([1, 3])]

预期产量:

[3, 0]

谁能帮我？

我有以下序列,它们是具有序列标题及其核苷酸的fasta格式.如何随机提取序列.例如,我想从总序列中随机选择2个序列.提供的工具是根据百分比而不是序列数提取.谁能帮我？

A.fasta

>chr1:1310706-1310726
GACGGTTTCCGGTTAGTGGAA
>chr1:901959-901979
GAGGGCTTTCTGGAGAAGGAG
>chr1:983001-983021
GTCCGCTTGCGGGACCTGGGG
>chr1:984333-984353
CTGGAATTCCGGGCGCTGGAG
>chr1:1154147-1154167
GAGATCGTCCGGGACCTGGGT

预期产出

>chr1:1154147-1154167
GAGATCGTCCGGGACCTGGGT
>chr1:901959-901979
GAGGGCTTTCTGGAGAAGGAG

我有这段代码生成以下输出:

result = []
with open('fileA.txt') as f:
    for line in f:
        if line.startswith('chr'):
            label = line.strip()
        elif line[0] == ' ':
            # short sequence
            length = len(line.strip())
            # find the index of the beginning of the short sequence
            for i, c in enumerate(line):
                if c.isalpha():
                    short_index = i
                    break
        elif line[0].isdigit():
            # long sequence
            n = line.split(' ')[0]
            # find the index of the beginning of the long sequence
            for i, c in enumerate(line):
                if c.isalpha():
                    long_index = i …

我想知道我们可以在一个数组中逐行读取.例如:

array([[ 0.28,  0.22,  0.23,  0.27],
       [ 0.12,  0.29,  0.34,  0.21],
       [ 0.44,  0.56,  0.51,  0.65]])

以数组形式读取第一行以执行某些操作,然后继续第二行数组:

array([0.28,0.22,0.23,0.27])

产生上述数组的原因是这两行代码:

from numpy import genfromtxt
single=genfromtxt('single.csv',delimiter=',')

single.csv

0.28,  0.22,  0.23,  0.27
0.12,  0.29,  0.34,  0.21
0.44,  0.56,  0.51,  0.65

使用readlines()看起来像生成列表而不是数组.就我而言,我正在使用csv文件.我试图逐行使用值行而不是一起使用它们以避免内存错误.谁能帮我？

with open('single.csv') as single:
    single=single.readlines()