TTTPOB

#!/usr/bin/env python3
import pysam
from collections import defaultdict
import subprocess
import click
from pathlib import Path
import pandas as pd
import numpy as np
from sys import stderr

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# from fastq_downloader.helper import construct_gsm_dict, download_and_verify, rename_files_by_run, merge_files
from fastq_downloader.helper.construct_gsm_dict import infotsv_to_dict, parse_acc_type
from fastq_downloader.helper.download_and_verify import (
    download_and_verify__,
    check_file,
)
from fastq_downloader.helper.rename_files_by_run import (
    write_filename_to_dict,
    actual_rename,
)

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#!python3
import click
import random


def read_chrom_size(chrom_size):
    chrom_size_dict = {}
    with open(chrom_size) as f:
        for line in f:
            line = line.strip().split()

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# save this script somewhere and invoke it in shell.nix shellHook
# it will read current r and radian path and write it to vscode
# workspace settings
# jq required
settings=.vscode/settings.json
mkdir -p .vscode
echo '{}' > $settings
rpath_exsits=$(cat $settings|jq '."r.rpath.linux"')
rterm_exsits=$(cat $settings|jq '."r.rterm.linux"')
not_exsist="null"

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#!/usr/bin/env Rscript
suppressPackageStartupMessages({
    library(tidyverse)
})
args <- commandArgs(trailingOnly = TRUE)
bed <- args[1]
distshift <- args[2] %>% as.numeric()
chromsize <- args[3]

# debug only

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bedcolname<- c(
    "seqnames",
    "start",
    "end",
    "name",
    "score",
    "strand"
)

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#!/usr/bin/env python3
import httpx
from bs4 import BeautifulSoup as bs
from xml.etree import ElementTree as ET
import click
import re

# see https://blog.tpob.xyz/2021/10/14/%E6%9B%B4%E5%BF%AB%E8%8E%B7%E5%BE%97srr-accession/
# for more information

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readComputeMatrixResult<-function(dfPath,offset=6){
  library(rjson)
  library(tidyverse)
  
  df<-read_tsv(file=dfPath,col_names=F,col_types=cols(),skip=1)
  metadata<-readLines(gzfile(dfPath),1)%>%str_remove("^@")%>%fromJSON(json_str=.)
  dfSplited<-list()
  for(i in 1:length(metadata$sample_labels)){
    dfSplited<-c(
      dfSplited,

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#!/bin/env python3
## the reason why i use urllib is to minimize dependency requiremnts
## the reason i dont user serverchan (https://sc.ftqq.com/) is that i want a multiuser support
from urllib import request
import sys
import json

## Please Change xxxxxx to the value you have
CORPID="xxxxxx"
MSGSECRET="xxxxxx"

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@namespace url(http://www.w3.org/1999/xhtml);

/*!
 * custom-yahei-family.css
 * https://n2o.io/go?page=custom.css
 *
 * Copyright 2018 Francis Zhao <francis@n2o.io>
 * https://n2o.io/license
 *
 * Date: 2018-03-11T15:00+06:00