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测序/生信分析

我们专注短读长测序平台的碱基识别（Basecall）任务。任务的关键特征是：

• 输入数据：$\mathbf{X} \in \mathcal{R}^{(T \times N \times C)}$，其中

  • $T$: 表示测序循环数目，范围在 $50 \sim 1000$
  • $N$: 表示 DNA 分子数目，范围在 $10^7 \sim 10^{11}$
  • $D$: 表示输入信号的维度，范围在 $2 \sim 10^2$

• 输出数据：$\mathbf{Y} \in \{a, t, c, g\}^{(N \times T)}$，即 N 条长度为 T 的基因序列

yangyushi

import numpy as np
import matplotlib.pyplot as plt
from matplotlib import cm


def get_transfer_mat(N, p, q):
    """
    Calculating the transition matrix P with shape (N, N).

    P_ij: the transition probability of two states:

yangyushi

sudo rm -rf Python-3.8.6
tar -xzf Python-3.8.6.tgz
cd Python-3.8.6

export LD_LIBRARY_PATH=/usr/local/lib
export LD_RUN_PATH=/usr/local/lib
./configure  --enable-optimizations --prefix=/usr/local\
    --enable-shared --enable-loadable-sqlite-extensions\
	CPPFLAGS="-I/usr/local/include -I/usr/local/include/openssl"\
	LDFLAGS="-L/usr/local/lib -L/usr/local/lib/openssl"

yangyushi

import numpy as np
from scipy import ndimage
import matplotlib.pyplot as plt


x = np.zeros((30, 30))

x[10, 10] = 1
x[20, 10] = 1
x[10, 20] = 1

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p1 = np.random.random((100, 2)) # feature points in camera 1
p2 = np.random.random((100, 2)) # feature points in camera 1

# camera matrices
k1 = np.random.random((3, 3))
k2 = np.random.random((3, 3))


# Method 1: calculate essential matrix (E) from the fundamental matrix (F)

yangyushi

#!/usr/bin/env python3
"""
This script demonstrated the way to link positions into trajectories
    and then calculate the MSD
"""
import numpy as np
import trackpy as tp
from itertools import product
import matplotlib.pyplot as plt
import pandas as pd

yangyushi

#!/usr/bin/env python3
"""
This script demonstrated the way to use low-level `link_iter` api
    from `trackpy` to link two successive frames.
"""
import numpy as np
import trackpy as tp
from itertools import product
import matplotlib.pyplot as plt
from matplotlib import cm

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yangyushi

#include <iostream>
#include <vector>

using namespace std;
using VVI = vector<vector<int>>;


template<class T>
void recursive_product(
    const vector<vector<T>>& arrays, vector<vector<T>>& result, int idx=0

yangyushi

Originall From: Posted 2015-05-29 http://ubwg.net/b/full-list-of-ffmpeg-flags-and-options

This is the complete list that’s outputted by ffmpeg when running ffmpeg -h full.

usage: ffmpeg [options] [[infile options] -i infile]… {[outfile options] outfile}…

Getting help:
    -h — print basic options
    -h long — print more options
    -h full — print all options (including all format and codec specific options, very long)