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1 #!/usr/bin/env python
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2
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3 import json
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4 import optparse
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5 import os
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6 import subprocess
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7 import sys
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8
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9 DEFAULT_DATA_TABLE_NAME = "malt_indices"
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10
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11
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12 def get_id_name(params, dbkey, fasta_description=None):
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13 sequence_id = params['param_dict']['sequence_id']
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14 if not sequence_id:
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15 sequence_id = dbkey
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16
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17 sequence_name = params['param_dict']['sequence_name']
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18 if not sequence_name:
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19 sequence_name = fasta_description
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20 if not sequence_name:
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21 sequence_name = dbkey
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22 return sequence_id, sequence_name
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23
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24
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25 def build_malt_index(data_manager_dict, fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, sequence_type, shapes, max_hits_per_seed, protein_reduct, data_table_name=DEFAULT_DATA_TABLE_NAME):
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26 fasta_base_name = os.path.split(fasta_filename)[-1]
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27 sym_linked_fasta_filename = os.path.join(target_directory, fasta_base_name)
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28 os.symlink(fasta_filename, sym_linked_fasta_filename)
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29 args = ['malt-build', '--input', sym_linked_fasta_filename, '--sequenceType', sequence_type, '--index', 'index']
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30 threads = os.environ.get('GALAXY_SLOTS')
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31 if threads:
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32 args.extend(['--threads', threads])
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33 if shapes is not None:
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34 args.extend('--shapes', shapes)
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35 if max_hits_per_seed is not None:
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36 args.extend('--maxHitsPerSeed', max_hits_per_seed)
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37 if protein_reduct is not None:
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38 args.extend('--proteinReduct', protein_reduct)
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39 proc = subprocess.Popen(args=args, shell=False, cwd=target_directory)
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40 return_code = proc.wait()
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41 if return_code:
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42 sys.exit('Error building index, return_code: %d' % return_code)
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43 data_table_entry = dict(value=sequence_id, dbkey=dbkey, name=sequence_name, path=fasta_base_name)
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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 parser = optparse.OptionParser()
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56 parser.add_option('-f', '--fasta_filename', dest='fasta_filename', action='store', type="string", help='fasta filename')
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57 parser.add_option('-d', '--fasta_dbkey', dest='fasta_dbkey', action='store', type="string", help='fasta dbkey')
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58 parser.add_option('-t', '--fasta_description', dest='fasta_description', action='store', type="string", default=None, help='fasta description')
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59 parser.add_option('-e', '--sequence_type', dest='sequence_type', action='store', type="string", help='DNA or Protein sequences')
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60 parser.add_option('-p', '--shapes', dest='shapes', action='store', type="string", default=None, help='Comma-separated list of seed shapes')
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61 parser.add_option('-m', '--max_hits_per_seed', dest='max_hits_per_seed', action='store', type="int", default=None, help='Maximum number of hits per seed')
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62 parser.add_option('-r', '--protein_reduct', dest='protein_reduct', action='store', type="string", default=None, help='Name or definition of protein alphabet reduction')
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63 (options, args) = parser.parse_args()
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64
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65 filename = args[0]
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66
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67 with open(filename) as fh:
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68 params = json.load(fh)
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69 target_directory = params['output_data'][0]['extra_files_path']
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70 os.mkdir(target_directory)
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71 data_manager_dict = {}
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72
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73 dbkey = options.fasta_dbkey
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74
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75 if dbkey in [None, '', '?']:
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76 raise Exception('"%s" is not a valid dbkey. You must specify a valid dbkey.' % (dbkey))
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77
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78 sequence_id, sequence_name = get_id_name(params, dbkey=dbkey, fasta_description=options.fasta_description)
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79
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80 # Build the index.
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81 build_malt_index(data_manager_dict, options.fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, options.sequence_type, options.shapes, options.max_hits_per_seed, options.protein_reduct, data_table_name=DEFAULT_DATA_TABLE_NAME)
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82
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83 # Save info to json file.
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84 with open(filename, 'w') as fh:
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85 json.dump(data_manager_dict, fh, sort_keys=True)
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86
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87
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88 if __name__ == "__main__":
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89 main()
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