Mercurial > repos > pimarin > data_manager_build_amrfinderplus

annotate data_manager/data_manager_build_amrfinderplus.py @ 1:75f79148cb06 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit dd78d1ba0f784a0a122159c4a6d192b8d65f6a8c-dirty
author pimarin
date Thu, 22 Dec 2022 09:51:41 +0000
parents 43ec3aadda50
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43ec3aadda50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 60348db40f25b746db8fd85d6d62ff7569ce28d3
pimarin
parents:
diff changeset
1 import argparse
43ec3aadda50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 60348db40f25b746db8fd85d6d62ff7569ce28d3
pimarin
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2 import json
43ec3aadda50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 60348db40f25b746db8fd85d6d62ff7569ce28d3
pimarin
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3 import os
43ec3aadda50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 60348db40f25b746db8fd85d6d62ff7569ce28d3
pimarin
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4 import subprocess as sp
43ec3aadda50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 60348db40f25b746db8fd85d6d62ff7569ce28d3
pimarin
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5 from ftplib import FTP
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75f79148cb06 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit dd78d1ba0f784a0a122159c4a6d192b8d65f6a8c-dirty
pimarin
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6 from io import BytesIO
75f79148cb06 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit dd78d1ba0f784a0a122159c4a6d192b8d65f6a8c-dirty
pimarin
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7 from pathlib import Path
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43ec3aadda50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 60348db40f25b746db8fd85d6d62ff7569ce28d3
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43ec3aadda50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 60348db40f25b746db8fd85d6d62ff7569ce28d3
pimarin
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9 import pandas as pd
43ec3aadda50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 60348db40f25b746db8fd85d6d62ff7569ce28d3
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43ec3aadda50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 60348db40f25b746db8fd85d6d62ff7569ce28d3
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43ec3aadda50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 60348db40f25b746db8fd85d6d62ff7569ce28d3
pimarin
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12 class GetAmrFinderPlusDataManager:
43ec3aadda50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 60348db40f25b746db8fd85d6d62ff7569ce28d3
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13 """
43ec3aadda50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 60348db40f25b746db8fd85d6d62ff7569ce28d3
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14 Create the json file with database information for galaxy data manager
43ec3aadda50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 60348db40f25b746db8fd85d6d62ff7569ce28d3
pimarin
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15 """
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16
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17 def __init__(self,
43ec3aadda50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 60348db40f25b746db8fd85d6d62ff7569ce28d3
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18 amrfinderplus_database="amrfinderplus_database",
43ec3aadda50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 60348db40f25b746db8fd85d6d62ff7569ce28d3
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19 db_name="amrfinderplus-db",
43ec3aadda50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 60348db40f25b746db8fd85d6d62ff7569ce28d3
pimarin
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20 amrfinderplus_version="latest",
43ec3aadda50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 60348db40f25b746db8fd85d6d62ff7569ce28d3
pimarin
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21 date_version=None):
43ec3aadda50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 60348db40f25b746db8fd85d6d62ff7569ce28d3
pimarin
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22 self.data_table_name = amrfinderplus_database
43ec3aadda50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 60348db40f25b746db8fd85d6d62ff7569ce28d3
pimarin
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23 self._db_name = db_name
43ec3aadda50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 60348db40f25b746db8fd85d6d62ff7569ce28d3
pimarin
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24 self._amrfinderplus_version = amrfinderplus_version
43ec3aadda50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 60348db40f25b746db8fd85d6d62ff7569ce28d3
pimarin
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25 self._amrfinderplus_date_version = date_version
43ec3aadda50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 60348db40f25b746db8fd85d6d62ff7569ce28d3
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26 self.data_table_entry = None
43ec3aadda50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 60348db40f25b746db8fd85d6d62ff7569ce28d3
pimarin
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27 self.amrfinderplus_table_list = None
43ec3aadda50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 60348db40f25b746db8fd85d6d62ff7569ce28d3
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28
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29 def get_data_table_format(self):
43ec3aadda50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 60348db40f25b746db8fd85d6d62ff7569ce28d3
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30 """
43ec3aadda50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 60348db40f25b746db8fd85d6d62ff7569ce28d3
pimarin
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31 Skeleton of a data_table format
43ec3aadda50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 60348db40f25b746db8fd85d6d62ff7569ce28d3
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32 return: a data table formatted for json output
43ec3aadda50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 60348db40f25b746db8fd85d6d62ff7569ce28d3
pimarin
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33 """
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34 self.data_table_entry = {
43ec3aadda50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 60348db40f25b746db8fd85d6d62ff7569ce28d3
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35 "data_tables": {
43ec3aadda50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 60348db40f25b746db8fd85d6d62ff7569ce28d3
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36 self.data_table_name: {}
43ec3aadda50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 60348db40f25b746db8fd85d6d62ff7569ce28d3
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37 }
43ec3aadda50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 60348db40f25b746db8fd85d6d62ff7569ce28d3
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38 }
43ec3aadda50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 60348db40f25b746db8fd85d6d62ff7569ce28d3
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39 return self.data_table_entry
43ec3aadda50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 60348db40f25b746db8fd85d6d62ff7569ce28d3
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40
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41 def get_data_manager(self):
43ec3aadda50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 60348db40f25b746db8fd85d6d62ff7569ce28d3
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42 """
43ec3aadda50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 60348db40f25b746db8fd85d6d62ff7569ce28d3
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43 Create the empty data table format and add all the information into
43ec3aadda50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 60348db40f25b746db8fd85d6d62ff7569ce28d3
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44 return: The data table with database information
43ec3aadda50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 60348db40f25b746db8fd85d6d62ff7569ce28d3
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45 """
43ec3aadda50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 60348db40f25b746db8fd85d6d62ff7569ce28d3
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46 self.amrfinderplus_table_list = self.get_data_table_format()
43ec3aadda50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 60348db40f25b746db8fd85d6d62ff7569ce28d3
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47 amrfinderplus_value = f"amrfinderplus_V{self._amrfinderplus_version}" \
43ec3aadda50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 60348db40f25b746db8fd85d6d62ff7569ce28d3
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48 f"_{self._amrfinderplus_date_version}"
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49 amrfinderplus_name = f"V{self._amrfinderplus_version}" \
43ec3aadda50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 60348db40f25b746db8fd85d6d62ff7569ce28d3
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50 f"-{self._amrfinderplus_date_version}"
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51 data_info = dict(value=amrfinderplus_value,
43ec3aadda50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 60348db40f25b746db8fd85d6d62ff7569ce28d3
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52 name=amrfinderplus_name,
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53 path=self._db_name)
43ec3aadda50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 60348db40f25b746db8fd85d6d62ff7569ce28d3
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54 self.amrfinderplus_table_list["data_tables"][self.data_table_name] = [data_info]
43ec3aadda50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 60348db40f25b746db8fd85d6d62ff7569ce28d3
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55 return self.amrfinderplus_table_list
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56
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57
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58 class DownloadAmrFinderPlusDatabase(GetAmrFinderPlusDataManager):
43ec3aadda50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 60348db40f25b746db8fd85d6d62ff7569ce28d3
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59 """
43ec3aadda50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 60348db40f25b746db8fd85d6d62ff7569ce28d3
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60 Download the amrfinderplus database from the ncbi.
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61 Make the database available with hmm and indexed files
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62 Build the data manager infos for galaxy
43ec3aadda50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 60348db40f25b746db8fd85d6d62ff7569ce28d3
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63 """
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64
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65 def __init__(self,
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66 output_dir=Path.cwd(),
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67 ncbi_url="ftp.ncbi.nlm.nih.gov",
43ec3aadda50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 60348db40f25b746db8fd85d6d62ff7569ce28d3
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68 ftp_login="anonymous",
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69 ftp_password="anonymous",
43ec3aadda50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 60348db40f25b746db8fd85d6d62ff7569ce28d3
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70 amrfinderplus_database="amrfinderplus_database",
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71 db_name="amrfinderplus-db",
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72 amrfinderplus_version="latest",
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73 json_file_path=None,
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74 date_version=None,
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75 amrfinderplus_db_path=None,
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76 test_mode=False):
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77
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78 super().__init__()
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79 self.json_file_path = json_file_path
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80 self._output_dir = output_dir
43ec3aadda50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 60348db40f25b746db8fd85d6d62ff7569ce28d3
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81 self._ncbi_ftp_url = ncbi_url
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82 self._ncbi_database_path = "pathogen/Antimicrobial_resistance/AMRFinderPlus/database"
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83 self._login = ftp_login
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84 self._password = ftp_password
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85 self._amrfinderplus_database = amrfinderplus_database
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86 self._db_name = db_name
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87 self._amrfinderplus_version = amrfinderplus_version
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88 self._amrfinderplus_date_version = date_version
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89 self.species_list = None
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90 self.test_mode = test_mode
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91 self.amrfinderplus_db_path = amrfinderplus_db_path
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92
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93 @staticmethod
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94 def subprocess_cmd(command, *args):
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95 """
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96 Method to call external tools with any parameters
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97 :param command: command name from the tool used (e.g. wget or makeblastdb)
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98 :param args: free number of argument need for the command tool (e.g. -r, -P ...)
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99 :return: launch the command line from the system
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100 """
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101 cmd = [command]
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102 [cmd.append(i) for i in args]
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103 proc = sp.run(cmd, stdout=sp.PIPE, stderr=sp.PIPE)
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104 if proc.returncode != 0:
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105 print(f'Error type {proc.returncode} with : \n {proc}')
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106
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107 def download_amrfinderplus_db(self):
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108 """
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109 Download the amrfinderplus database from the ncbi ftp server
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110 """
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111 self.amrfinderplus_db_path = f'{self._output_dir}/{self._db_name}'
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112 os.makedirs(self.amrfinderplus_db_path)
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113 if self._amrfinderplus_version == 'latest':
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114 self.get_amrfinderplus_version()
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115
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116 amrfinderplus_ftp_path = f"ftp://{self._login}:" \
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117 f"{self._password}@{self._ncbi_ftp_url}/" \
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118 f"{self._ncbi_database_path}/" \
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119 f"{self._amrfinderplus_version}/" \
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120 f"{self._amrfinderplus_date_version}"
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121 if self.test_mode is True:
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122 file_list = ["AMR_DNA-Escherichia", "version.txt", "taxgroup.tab", "database_format_version.txt"]
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123 output_option = "-O"
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124 for file in file_list:
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125 self.subprocess_cmd("wget",
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126 "-nd",
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127 "-np",
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128 "-r",
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129 f"{amrfinderplus_ftp_path}/{file}",
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130 output_option,
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131 f"{self.amrfinderplus_db_path}/{file}")
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132 else:
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133 output_option = "-P"
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134 self.subprocess_cmd("wget",
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135 "-nd",
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136 "-np",
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137 "-r",
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138 amrfinderplus_ftp_path,
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139 output_option,
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140 self.amrfinderplus_db_path)
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141
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142 def make_hmm_profile(self):
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143 """
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144 Make the hmm profile using the AMR.LIB file previously download
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145 """
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146 hmm_file = Path(f"{self.amrfinderplus_db_path}/AMR.LIB")
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147 if Path.exists(hmm_file) and self.test_mode is False:
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148 self.subprocess_cmd("hmmpress", "-f", hmm_file)
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149 else:
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150 print("hmm_file file is missing to make hmm profiles")
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151
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152 def extract_filelist_makeblast(self):
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153 """
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154 Extract le list of species which have file in the database
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155 return: a filtered species list of available species in the database
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156 """
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157 taxa_group_path = Path(f"{self.amrfinderplus_db_path}/taxgroup.tab")
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158 if Path.exists(taxa_group_path):
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159 taxa_table = pd.read_table(taxa_group_path)
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160 taxa_table.columns = ["taxgroup", "gpipe_taxgroup", "number_of_nucl_ref_genes"]
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161 taxa_df = taxa_table[taxa_table.number_of_nucl_ref_genes > 0].filter(items=["taxgroup"], axis=1)
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162 if self.test_mode is True:
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163 taxa_df = taxa_df[taxa_df.taxgroup == "Escherichia"].taxgroup
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164 else:
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165 taxa_df = taxa_df.taxgroup
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166 self.species_list = list(taxa_df)
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167 else:
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168 print("taxgroup.tab file is missing to list available species")
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169
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170 def make_blastdb(self):
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171 """
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172 Index fasta file for blast
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173 """
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174 self.extract_filelist_makeblast()
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175 nucl_file_db_list = [f'{self.amrfinderplus_db_path}/AMR_DNA-{specie}' for specie in self.species_list]
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176 amr_dna = f'{self.amrfinderplus_db_path}/AMR_CDS'
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177 amr_prot = f'{self.amrfinderplus_db_path}/AMRProt'
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178 os.chdir(self.amrfinderplus_db_path)
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179 if Path(amr_dna).exists():
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180 nucl_file_db_list.append(amr_dna)
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181 else:
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182 print("No file AMR_CDS detected for indexing")
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183 if Path(amr_prot).exists():
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184 self.subprocess_cmd("makeblastdb", "-in", amr_prot, "-dbtype", "prot")
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185 else:
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186 print("No file AMRProt detected for indexing")
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187 [self.subprocess_cmd("makeblastdb", "-in", file, "-dbtype", "nucl") for file in nucl_file_db_list]
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188
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189 def get_amrfinderplus_version(self, version_file="version.txt",
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190 database_version_file="database_format_version.txt"):
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191 """
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192 Check the version when latest if provided and update the number
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193 param version_file: name of the file containing version information
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194 param database_version_file: name of the file containing date version information
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195 """
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196 ftp = FTP(self._ncbi_ftp_url)
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197 ftp.login(self._login, self._password)
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198 ftp.cwd(f"{self._ncbi_database_path}/{self._amrfinderplus_version}")
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199 db_version = BytesIO()
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200 db_date_version = BytesIO()
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201 ftp.retrbinary(f'RETR {version_file}', db_version.write)
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202 ftp.retrbinary(f'RETR {database_version_file}', db_date_version.write)
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203 self._amrfinderplus_date_version = db_version.getvalue().decode("utf-8").splitlines()[0]
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204 self._amrfinderplus_version = '.'.join(
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205 db_date_version.getvalue().decode("utf-8").splitlines()[0].split(".")[:2])
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206
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207 def read_json_input_file(self):
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208 """
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209 Import the json file
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210 """
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211 with open(self.json_file_path) as fh:
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212 params = json.load(fh)
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213 target_dir = params['output_data'][0]['extra_files_path']
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214 os.makedirs(target_dir)
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215 self._output_dir = target_dir
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216
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217 def write_json_infos(self):
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218 """
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219 Write in the imported json file
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220 """
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221 with open(self.json_file_path, 'w') as fh:
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222 json.dump(self.get_data_manager(), fh, sort_keys=True)
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223
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224
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225 def parse_arguments():
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226 """
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227 List of arguments provided by the user
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228 return: parsed arguments
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229 """
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230 # parse options and arguments
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231 arg_parser = argparse.ArgumentParser()
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232 arg_parser.add_argument("data_manager_json",
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233 help="json file from galaxy")
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234 arg_parser.add_argument("--db_version", default="latest",
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235 help="select the major version of the database (e.g. 3.10, 3.8), default is latest")
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236 arg_parser.add_argument("--db_date",
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237 help="select the date into the database version (e.g. 2022-10-11.2)")
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238 arg_parser.add_argument("--test", action='store_true',
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239 help="option to test the script with an lighted database")
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240 return arg_parser.parse_args()
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241
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242
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243 def main():
43ec3aadda50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 60348db40f25b746db8fd85d6d62ff7569ce28d3
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244 all_args = parse_arguments()
43ec3aadda50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 60348db40f25b746db8fd85d6d62ff7569ce28d3
pimarin
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245 amrfinderplus_download = DownloadAmrFinderPlusDatabase(amrfinderplus_version=all_args.db_version,
43ec3aadda50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 60348db40f25b746db8fd85d6d62ff7569ce28d3
pimarin
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246 date_version=all_args.db_date,
43ec3aadda50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 60348db40f25b746db8fd85d6d62ff7569ce28d3
pimarin
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247 json_file_path=all_args.data_manager_json,
43ec3aadda50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 60348db40f25b746db8fd85d6d62ff7569ce28d3
pimarin
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248 test_mode=all_args.test)
43ec3aadda50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 60348db40f25b746db8fd85d6d62ff7569ce28d3
pimarin
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249 amrfinderplus_download.read_json_input_file()
43ec3aadda50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 60348db40f25b746db8fd85d6d62ff7569ce28d3
pimarin
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250 amrfinderplus_download.download_amrfinderplus_db()
43ec3aadda50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 60348db40f25b746db8fd85d6d62ff7569ce28d3
pimarin
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251 amrfinderplus_download.make_hmm_profile()
43ec3aadda50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 60348db40f25b746db8fd85d6d62ff7569ce28d3
pimarin
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252 amrfinderplus_download.make_blastdb()
43ec3aadda50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 60348db40f25b746db8fd85d6d62ff7569ce28d3
pimarin
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253 amrfinderplus_download.write_json_infos()
43ec3aadda50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 60348db40f25b746db8fd85d6d62ff7569ce28d3
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254
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255
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pimarin
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256 if __name__ == '__main__':
43ec3aadda50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 60348db40f25b746db8fd85d6d62ff7569ce28d3
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257 main()