71 lines
2.7 KiB
Python
Executable File
71 lines
2.7 KiB
Python
Executable File
import argparse
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import json
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import os
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import subprocess
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import time
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def run(barcode, normal, umi, input_dir, output_dir, project, bed, wdl):
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input_dir = os.path.realpath(input_dir)
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output_dir = os.path.realpath(output_dir)
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wdl = os.path.realpath(wdl)
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arg = {
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"pipeline.tumor": barcode,
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"pipeline.normal": normal,
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"pipeline.umi": umi,
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"pipeline.input_dir": input_dir,
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"pipeline.output_dir": output_dir,
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"pipeline.project": project,
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"pipeline.bed": bed
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}
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arg = {key: value for key, value in arg.items() if value not in (None, '', False)}
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# generate json
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jsfile_path = os.path.join(output_dir, f'{barcode}.json')
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with open(jsfile_path, 'w') as jsfile:
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jsfile.write(json.dumps(arg, indent=4, ensure_ascii=False))
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# run pipeline
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cmd1 = 'export PATH=/home/zhangchao/project/pipeline/workflow/script:$PATH'
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cmd2 = 'export PUBLIC=/home/zhangchao/project/pipeline/workflow/script/public/'
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cmd3 = f'cd {output_dir}'
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cmd4 = f'/home/zhangchao/soft/jdk-17.0.7+7/bin/java -jar /home/zhangchao/soft/cromwell-85.jar run --inputs {jsfile_path} {wdl}'
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cmd = f'{cmd1}; {cmd2}; {cmd3}; {cmd4}'
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# 记录开始时间
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start_time = time.time()
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print(cmd)
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ret = subprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE, encoding="utf-8")
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pidnum = ret.pid
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with open(os.path.join(output_dir, 'pid'), 'w') as pidfile:
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pidfile.write(str(pidnum))
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ret.wait()
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# 记录结束时间
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end_time = time.time()
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# 计算运行时间
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elapsed_time = end_time - start_time
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print("\n运行时间：{:.2f} 秒".format(elapsed_time))
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print(ret.stdout.read(), ret.stderr.read())
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print('#' * 50)
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print('读取日志')
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if __name__ == '__main__':
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parser = argparse.ArgumentParser(description="JM to run pipeline")
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parser.add_argument('-n', '--barcode', help="sample's barcode", required=True)
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parser.add_argument('-s', '--normal', help="sample's normal", default='', required=False, nargs='?')
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parser.add_argument('-u', '--umi', action='store_true', help="is umi sample", default=False)
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parser.add_argument('-i', '--input_dir', help="sample's input_dir/workdir", required=True)
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parser.add_argument('-o', '--output_dir', help="Output directory, default ./", default='./')
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parser.add_argument('-p', '--project', help="project", required=True)
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parser.add_argument('-b', '--bed', help="bed", required=True)
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parser.add_argument('-w', '--wdl', help="wdl")
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args = parser.parse_args()
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run(args.barcode, args.normal, args.umi, args.input_dir, args.output_dir, args.project, args.bed, args.wdl)
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