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1 #!/usr/bin/env python
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2 # Based heavily on the HISAT2 data manager wrapper
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3
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4 import argparse
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5 import os
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6 import shlex
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7 import subprocess
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8 import sys
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9 from json import dumps, loads
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10
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11 DEFAULT_DATA_TABLE_NAME = "bwameth_indexes"
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12
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13
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14 def build_hisat_index(data_manager_dict, params, args):
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15 data_table_name = args.data_table_name
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16 target_directory = params[ 'output_data' ][0]['extra_files_path']
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17 if not os.path.exists( target_directory ):
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18 os.mkdir( target_directory )
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19 fasta_base_name = os.path.basename(args.fasta_filename)
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20 sym_linked_fasta_filename = os.path.join(target_directory, fasta_base_name)
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21 os.symlink(options.fasta_filename, sym_linked_fasta_filename)
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22 args = ['bwameth.py', 'index', sym_linked_fasta_filename]
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23 proc = subprocess.Popen( args=args, shell=False, cwd=target_directory )
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24 return_code = proc.wait()
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25 if return_code:
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26 print >> sys.stderr, "Error building index."
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27 sys.exit( return_code )
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28 data_table_entry = dict(value=args.name, dbkey=args.dbkey, name=args.name, path=sequence_id)
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29 _add_data_table_entry(data_manager_dict, data_table_name, data_table_entry)
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30
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31
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32 def _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ):
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33 data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
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34 data_manager_dict['data_tables'][ data_table_name ] = data_manager_dict['data_tables'].get( data_table_name, [] )
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35 data_manager_dict['data_tables'][ data_table_name ].append( data_table_entry )
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36 return data_manager_dict
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37
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38
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39 def main():
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40 # Parse Command Line
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41 parser = argparse.ArgumentParser()
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42 parser.add_argument( '--output', default=None )
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43 parser.add_argument( '--fasta_filename', default=None )
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44 parser.add_argument( '--dbkey', default=None )
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45 parser.add_argument( '--name', default=None )
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46 parser.add_argument( '--description', default=None )
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47 parser.add_argument( '--data_table_name', default=DEFAULT_DATA_TABLE_NAME )
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48 args = parser.parse_args()
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49
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50 filename = args.output
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51 params = loads(open(filename).read())
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52 data_manager_dict = {}
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53
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54 if args.dbkey in [ None, '', '?' ]:
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55 raise Exception('"%s" is not a valid dbkey. You must specify a valid dbkey.' % (args.dbkey))
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56
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57 # build the index
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58 build_hisat_index(data_manager_dict, args)
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59
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60 # save info to json file
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61 open(filename, 'wb').write(dumps(data_manager_dict))
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62
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63 if __name__ == "__main__":
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64 main()
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