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1 #!/usr/bin/env python
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2 # Based heavily on the kallisto data manager wrapper script by iuc
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3 from __future__ import print_function
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4
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5 import argparse
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6 import os
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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 = "salmon_indexes"
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12
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13
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14 def get_id_name( params, dbkey, fasta_description=None):
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15 # TODO: ensure sequence_id is unique and does not already appear in location file
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16 sequence_id = params['param_dict']['sequence_id']
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17 if not sequence_id:
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18 sequence_id = dbkey
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19
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20 sequence_name = params['param_dict']['sequence_name']
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21 if not sequence_name:
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22 sequence_name = fasta_description
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23 if not sequence_name:
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24 sequence_name = dbkey
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25 return sequence_id, sequence_name
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26
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27
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28 def build_salmon_index( data_manager_dict, options, params, sequence_id, sequence_name ):
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29 data_table_name = options.data_table_name or DEFAULT_DATA_TABLE_NAME
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30 target_directory = params[ 'output_data' ][0]['extra_files_path']
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31 if not os.path.exists( target_directory ):
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32 os.mkdir( target_directory )
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2
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33 args = [ 'salmon', 'index' ]
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1
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34 if options.kmer_size != '':
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35 args.append('-k')
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36 args.append(options.kmer_size)
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37 args.extend( [ '-t' , options.fasta_filename, '-i', sequence_id ] )
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38 proc = subprocess.Popen( args=args, shell=False, cwd=target_directory )
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39 return_code = proc.wait()
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40 if return_code:
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41 print("Error building index.", file=sys.stderr)
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42 sys.exit( return_code )
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43 data_table_entry = dict( value=sequence_id, dbkey=options.fasta_dbkey, name=sequence_name, path=sequence_id )
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44 _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry )
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45
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46
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47 def _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ):
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48 data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
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49 data_manager_dict['data_tables'][ data_table_name ] = data_manager_dict['data_tables'].get( data_table_name, [] )
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50 data_manager_dict['data_tables'][ data_table_name ].append( data_table_entry )
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51 return data_manager_dict
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52
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53
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54 def main():
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55 # Parse Command Line
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56 parser = argparse.ArgumentParser()
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57 parser.add_argument( '--output', dest='output', action='store', type=str, default=None )
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58 parser.add_argument( '--fasta_filename', dest='fasta_filename', action='store', type=str, default=None )
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59 parser.add_argument( '--fasta_dbkey', dest='fasta_dbkey', action='store', type=str, default=None )
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60 parser.add_argument( '--fasta_description', dest='fasta_description', action='store', type=str, default=None )
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61 parser.add_argument( '--data_table_name', dest='data_table_name', action='store', type=str, default='salmon_indexes' )
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62 parser.add_argument( '-k', '--kmer_size', dest='kmer_size', action='store', type=str, help='kmer_size' )
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63 options = parser.parse_args()
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64
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65 filename = options.output
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66
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67 params = loads( open( filename ).read() )
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68 data_manager_dict = {}
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69
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70 if options.fasta_dbkey in [ None, '', '?' ]:
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71 raise Exception( '"%s" is not a valid dbkey. You must specify a valid dbkey.' % ( options.fasta_dbkey ) )
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72
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73 sequence_id, sequence_name = get_id_name( params, dbkey=options.fasta_dbkey, fasta_description=options.fasta_description )
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74
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75 # build the index
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76 build_salmon_index( data_manager_dict, options, params, sequence_id, sequence_name )
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77
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78 # save info to json file
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79 open( filename, 'w' ).write( dumps( data_manager_dict ) )
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80
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81
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82 if __name__ == "__main__":
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83 main()
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