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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
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10 def get_id_name(params, dbkey, fasta_description=None):
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11 sequence_id = params['param_dict']['sequence_id']
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12 if not sequence_id:
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13 sequence_id = dbkey
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14
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15 sequence_name = params['param_dict']['sequence_name']
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16 if not sequence_name:
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17 sequence_name = fasta_description
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18 if not sequence_name:
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19 sequence_name = dbkey
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20 return sequence_id, sequence_name
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21
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22
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1
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23 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):
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24 # The malt-build program produces a directory of files,
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25 # so the data table path entry will be a directory and
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26 # not an index file.
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27 fasta_base_name = os.path.split(fasta_filename)[-1]
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28 sym_linked_fasta_filename = os.path.join(target_directory, fasta_base_name)
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29 os.symlink(fasta_filename, sym_linked_fasta_filename)
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30 args = ['malt-build', '--input', sym_linked_fasta_filename, '--sequenceType', sequence_type, '--index', target_directory]
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31 threads = os.environ.get('GALAXY_SLOTS')
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32 if threads:
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33 args.extend(['--threads', threads])
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34 if shapes is not None:
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1
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35 args.extend(['--shapes', shapes])
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36 if max_hits_per_seed is not None:
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1
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37 args.extend(['--maxHitsPerSeed', max_hits_per_seed])
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38 if protein_reduct is not None:
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39 args.extend(['--proteinReduct', protein_reduct])
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40 proc = subprocess.Popen(args=args, shell=False, cwd=target_directory)
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41 return_code = proc.wait()
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42 if return_code:
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43 sys.exit('Error building index, return_code: %d' % return_code)
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1
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44 # Remove unwanted files from the output directory.
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45 os.remove(sym_linked_fasta_filename)
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46 # The path entry here is the directory
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47 # where the index files will be located,
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48 # not a single index file (malt-build
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49 # produces a directory if files, which
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50 # is considered an index..
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51 data_table_entry = dict(value=sequence_id, dbkey=dbkey, name=sequence_name, path=None)
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52 _add_data_table_entry(data_manager_dict, data_table_entry)
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53
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54
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1
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55 def _add_data_table_entry(data_manager_dict, data_table_entry):
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56 data_table_name = "malt_indices"
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57 data_manager_dict['data_tables'] = data_manager_dict.get('data_tables', {})
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58 data_manager_dict['data_tables'][data_table_name] = data_manager_dict['data_tables'].get(data_table_name, [])
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59 data_manager_dict['data_tables'][data_table_name].append(data_table_entry)
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60 return data_manager_dict
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61
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62
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63 def main():
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64 parser = optparse.OptionParser()
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65 parser.add_option('-f', '--fasta_filename', dest='fasta_filename', action='store', type="string", help='fasta filename')
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66 parser.add_option('-d', '--fasta_dbkey', dest='fasta_dbkey', action='store', type="string", help='fasta dbkey')
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67 parser.add_option('-t', '--fasta_description', dest='fasta_description', action='store', type="string", default=None, help='fasta description')
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68 parser.add_option('-e', '--sequence_type', dest='sequence_type', action='store', type="string", help='DNA or Protein sequences')
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69 parser.add_option('-p', '--shapes', dest='shapes', action='store', type="string", default=None, help='Comma-separated list of seed shapes')
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70 parser.add_option('-m', '--max_hits_per_seed', dest='max_hits_per_seed', action='store', type="string", default=None, help='Maximum number of hits per seed')
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71 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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72 (options, args) = parser.parse_args()
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73
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74 filename = args[0]
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75
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76 with open(filename) as fh:
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77 params = json.load(fh)
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78 target_directory = params['output_data'][0]['extra_files_path']
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79 os.mkdir(target_directory)
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80 data_manager_dict = {}
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81
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82 dbkey = options.fasta_dbkey
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83
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84 if dbkey in [None, '', '?']:
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85 raise Exception('"%s" is not a valid dbkey. You must specify a valid dbkey.' % (dbkey))
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86
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87 sequence_id, sequence_name = get_id_name(params, dbkey=dbkey, fasta_description=options.fasta_description)
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88
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89 # Build the index.
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90 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)
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91
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92 # Save info to json file.
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93 with open(filename, 'w') as fh:
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94 json.dump(data_manager_dict, fh, sort_keys=True)
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95
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96
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97 if __name__ == "__main__":
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98 main()
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