Custom_tools/encodeDownload at main · fatyang799/Custom_tools · GitHub

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#!/bin/bash

datatype=$1
url=$2
output_dir=$3
scipt_name=$4

# 使用说明
if [[ -z ${url} ]]; then
	echo "Usage: "
	echo -e "\t\$1: 你希望将下载fastq文件的实验类型，可以是ChIPseq、RNAseq、ATACseq、DNase、WGBS、Annotation等，不区分大小写"
	echo -e "\t\$2: 输入包含有所有你想要爬取数据的网站，例如 https://www.encodeproject.org/search/?type=Experiment&status=released&biosample_ontology.term_name=H1&target.label=H3K4me3"
	echo -e "\t\$3: 在下载对应文件（如fastq或者annotation.gz）的脚本中，下载文件保存的路径，并且下载对应文件的md5值也会保存在此处，如果不写，默认为 ./"
	echo -e "\t\$4: 下载文件的脚本名称，如果不写，默认为 download.sh"
	exit 100
fi

# 定义函数检查命令运行结果
function stat_check {
	stat=$?
	if [[ $stat -eq 0 ]]; then
		echo $1
	fi
	if [[ $stat -ne 0 ]]; then
		echo $2
		exit 100
	fi
}

# 脚本检查
if true; then
	if [[ ${datatype,,} != "chipseq" && ${datatype,,} != "rnaseq" && ${datatype,,} != "atacseq" && ${datatype,,} != "dnase" && ${datatype,,} != "wgbs" && ${datatype,,} != "annotation" ]]; then
		echo "The $1 parameter raise error, you can only input ChIPseq, RNAseq, ATACseq DNase WGBS or Annotation"
		exit 100
	fi
fi

# 参数检查
if true; then
	if [[ -z ${output_dir} ]]; then
		output_dir=./
	fi
	if [[ -z ${scipt_name} ]]; then
		scipt_name=download.sh
	fi
fi


# 爬取数据
if true; then
	python $HOME/Program/Custom_tools/encode/${datatype,,}/1.get_all_accession_ID.py ${url}
	stat_check "step1 successfully done." "step1 raise error."

	python $HOME/Program/Custom_tools/encode/${datatype,,}/2.get_download_info_according_to_ID.py
	stat_check "step2 successfully done." "step2 raise error."

	if [[ ${datatype,,} != "annotation" ]]; then
		python $HOME/Program/Custom_tools/encode/${datatype,,}/3.CT_file_for_Experiment.py
		stat_check "step3 successfully done." "step3 raise error."

		bash $HOME/Program/Custom_tools/encode/${datatype,,}/4.get_download_md5.sh ${output_dir} ${scipt_name}
		stat_check "step4 successfully done." "step4 raise error."
	else
		bash $HOME/Program/Custom_tools/encode/${datatype,,}/3.get_download_md5.sh ${output_dir} ${scipt_name}
		stat_check "step3 successfully done." "step4 raise error."
	fi
fi