Mercurial > repos > devteam > data_manager_bowtie2_index_builder

annotate data_manager/bowtie2_index_builder.py @ 11:2699da480b0b draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 7d38fdb04fe85a3934d4e2f611106837b6d3b35b"
author iuc
date Mon, 01 Nov 2021 07:22:42 +0000
parents e816eef8a48f
children
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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_NAMES = ["bowtie2_indexes"]
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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_bowtie2_index(data_manager_dict, fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, data_table_names=DEFAULT_DATA_TABLE_NAMES):
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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 sym_linked_fasta_filename = os.path.join(target_directory, fasta_base_name)
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32 os.symlink(fasta_filename, sym_linked_fasta_filename)
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33 args = ['bowtie2-build', sym_linked_fasta_filename, sequence_id]
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34 threads = os.environ.get('GALAXY_SLOTS')
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35 if threads:
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36 args.extend(['--threads', threads])
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37 proc = subprocess.Popen(args=args, shell=False, cwd=target_directory)
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38 return_code = proc.wait()
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39 if return_code:
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40 print("Error building index.", file=sys.stderr)
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41 sys.exit(return_code)
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42 data_table_entry = dict(value=sequence_id, dbkey=dbkey, name=sequence_name, path=sequence_id)
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43 for data_table_name in data_table_names:
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44 _add_data_table_entry(data_manager_dict, data_table_name, data_table_entry)
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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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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", default=None, help='fasta_filename')
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57 parser.add_option('-d', '--fasta_dbkey', dest='fasta_dbkey', action='store', type="string", default=None, 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('-n', '--data_table_name', dest='data_table_name', action='append', type="string", default=None, help='data_table_name')
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60 (options, args) = parser.parse_args()
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61
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62 filename = args[0]
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64 with open(filename) as fh:
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65 params = json.load(fh)
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66 target_directory = params['output_data'][0]['extra_files_path']
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67 os.mkdir(target_directory)
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68 data_manager_dict = {}
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70 dbkey = options.fasta_dbkey
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72 if dbkey in [None, '', '?']:
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73 raise Exception('"%s" is not a valid dbkey. You must specify a valid dbkey.' % (dbkey))
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75 sequence_id, sequence_name = get_id_name(params, dbkey=dbkey, fasta_description=options.fasta_description)
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77 # build the index
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78 build_bowtie2_index(data_manager_dict, options.fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, data_table_names=options.data_table_name or DEFAULT_DATA_TABLE_NAMES)
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80 # save info to json file
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81 with open(filename, 'w') as fh:
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82 json.dump(data_manager_dict, fh, sort_keys=True)
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85 if __name__ == "__main__":
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86 main()