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1 import argparse
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2 import os
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3 import json
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4 import re
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5 import pprint
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6 import subprocess
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7 import sys
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8
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9 if __name__ == "__main__":
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10 parser = argparse.ArgumentParser(description="Use VEP INSTALL.pl to download/process the cache for an assembly")
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11 parser.add_argument("--output-file")
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12 parser.add_argument("--output-dir")
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13 parser.add_argument("--assembly")
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14 args = parser.parse_args()
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15
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16 output_file = args.output_file
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17 output_dir = args.output_dir
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18 assembly = args.assembly
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19 extra = args.assembly
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20
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21 with open(output_file) as output_file_handle:
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22 params = json.loads(output_file_handle.read())
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23
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24 print(output_file)
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25 print(output_dir)
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26 print(assembly)
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27 pprint.pprint(params)
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28
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29 if not os.path.exists(output_dir):
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30 os.makedirs(output_dir)
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31
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32 vep_install_cmd = ["vep_install", "--NO_HTSLIB", "-a alcf", "--CACHEDIR", output_dir, "--SPECIES", assembly]
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33 vep_install_cmd = "vep_install --NO_HTSLIB -a alcf --CACHEDIR {0} --SPECIES {1}".format(output_dir, assembly)
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34 print("Running INSTALL.pl")
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35 #print(" ".join(vep_install_cmd))
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36 print(vep_install_cmd)
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37 exit_code = subprocess.call(vep_install_cmd, cwd=output_dir, shell=True)
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38 #process = subprocess.Popen(vep_install_cmd, shell=True, cwd=output_dir)
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39
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40 print(exit_code)
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41
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42 output_dict = dict(
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43 data_tables=dict(
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44 vep_cache_data=[{
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45 "path": output_dir,
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46 "dbkey": assembly,
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47 "name": assembly,
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48 "value": assembly
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49 }]
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50 )
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51 )
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52 with open(output_file, 'w') as output_file_handle:
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53 output_file_handle.write(json.dumps(output_dict))
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54 sys.exit(0) |
