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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 096286097ed5cdf189a1b68c3fc34d10f4142e54
author iuc
date Sun, 16 Apr 2023 08:28:16 +0000
parents acaa6719a478
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1 #!/usr/bin/env python
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2 # Dan Blankenberg
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3 from __future__ import print_function
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5 import json
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6 import optparse
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7 import os
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8 import subprocess
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9 import sys
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11 DEFAULT_DATA_TABLE_NAME = "picard_indexes"
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12
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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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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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28 def build_picard_index(data_manager_dict, fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, data_table_name=DEFAULT_DATA_TABLE_NAME):
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29 # TODO: allow multiple FASTA input files
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30 fasta_base_name = os.path.split(fasta_filename)[-1]
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31 prefix = os.path.splitext(fasta_base_name)[0]
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32 sym_linked_fasta_filename = os.path.join(target_directory, fasta_base_name)
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33 os.symlink(fasta_filename, sym_linked_fasta_filename)
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34 args = ['picard', 'CreateSequenceDictionary', 'R=%s' % sym_linked_fasta_filename, 'O=%s.dict' % prefix]
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35 proc = subprocess.Popen(args=args, shell=False, cwd=target_directory)
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36 return_code = proc.wait()
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37 if return_code:
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38 print("Error building index.", file=sys.stderr)
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39 sys.exit(return_code)
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40 data_table_entry = dict(value=sequence_id, dbkey=dbkey, name=sequence_name, path=fasta_base_name)
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41 _add_data_table_entry(data_manager_dict, data_table_name, data_table_entry)
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44 def _add_data_table_entry(data_manager_dict, data_table_name, data_table_entry):
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45 data_manager_dict['data_tables'] = data_manager_dict.get('data_tables', {})
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46 data_manager_dict['data_tables'][data_table_name] = data_manager_dict['data_tables'].get(data_table_name, [])
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47 data_manager_dict['data_tables'][data_table_name].append(data_table_entry)
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48 return data_manager_dict
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51 def main():
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52 parser = optparse.OptionParser()
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53 parser.add_option('-f', '--fasta_filename', dest='fasta_filename', action='store', type="string", default=None, help='fasta_filename')
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54 parser.add_option('-d', '--fasta_dbkey', dest='fasta_dbkey', action='store', type="string", default=None, help='fasta_dbkey')
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55 parser.add_option('-t', '--fasta_description', dest='fasta_description', action='store', type="string", default=None, help='fasta_description')
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56 parser.add_option('-n', '--data_table_name', dest='data_table_name', action='store', type="string", default=None, help='data_table_name')
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57 (options, args) = parser.parse_args()
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59 filename = args[0]
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61 with open(filename) as fh:
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62 params = json.load(fh)
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63 target_directory = params['output_data'][0]['extra_files_path']
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64 os.mkdir(target_directory)
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65 data_manager_dict = {}
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67 dbkey = options.fasta_dbkey
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69 if dbkey in [None, '', '?']:
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70 raise Exception('"%s" is not a valid dbkey. You must specify a valid dbkey.' % (dbkey))
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72 sequence_id, sequence_name = get_id_name(params, dbkey=dbkey, fasta_description=options.fasta_description)
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74 # build the index
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75 build_picard_index(data_manager_dict, options.fasta_filename, params, target_directory, dbkey, sequence_id,
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76 sequence_name, data_table_name=options.data_table_name or DEFAULT_DATA_TABLE_NAME)
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78 # save info to json file
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79 with open(filename, 'w') as fh:
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80 json.dump(data_manager_dict, fh, sort_keys=True)
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83 if __name__ == "__main__":
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84 main()