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1 #!/usr/bin/env python
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2 # ref: https://galaxyproject.org/admin/tools/data-managers/how-to/define/
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3
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4 import sys
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5 import os
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6 import tempfile
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7 import shutil
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8 import argparse
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9 import urllib2
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10 import tarfile
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11
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12 from galaxy.util.json import from_json_string, to_json_string
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13
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14 CHUNK_SIZE = 2**20 #1mb
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15
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16 def cleanup_before_exit(tmp_dir):
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17 if tmp_dir and os.path.exists(tmp_dir):
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18 shutil.rmtree(tmp_dir)
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19
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20 def stop_err(msg):
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21 sys.stderr.write(msg)
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22 sys.exit(1)
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23
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24 def get_reference_id_name(params):
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25 genome_id = params['param_dict']['genome_id']
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26 genome_name = params['param_dict']['genome_name']
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27 return genome_id, genome_name
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28
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5
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29 def get_url(params):
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30 trained_url = params['param_dict']['trained_url']
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31 return trained_url
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32
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33 def download_from_GlimmerHMM(data_manager_dict, target_directory, sequence_id, sequence_name, trained_dir):
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34 if not trained_dir:
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35 trained_dir = 'ftp://ccb.jhu.edu/pub/software/glimmerhmm/GlimmerHMM-3.0.4.tar.gz'
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36 #Download trained data, ref: https://dzone.com/articles/how-download-file-python
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37 f = urllib2.urlopen(trained_dir)
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38 data = f.read()
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39 downloadpath = 'tmp'
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40 os.mkdir(downloadpath)
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41 filepath = os.path.join(downloadpath, 'GlimmerHMM-3.0.4.tar')
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42 with open(filepath, 'wb') as code:
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43 code.write(data)
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44 with tarfile.open(filepath, mode='r:*') as tar:
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1
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45 subdir = [
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46 tarinfo for tarinfo in tar.getmembers()
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47 if sequence_id in tarinfo.name
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48 ]
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49 tar.extractall(members=subdir)
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5
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50 GlimmerHMM_TRAINED_DIR = os.path.join(downloadpath, 'GlimmerHMM', 'trained_dir', sequence_id)
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51 glimmerhmm_trained_target_dir = os.path.join(target_directory, sequence_id)
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52 shutil.copytree(GlimmerHMM_TRAINED_DIR, glimmerhmm_trained_target_dir)
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53 data_table_entry = dict(value=sequence_id, name=sequence_name, path=glimmerhmm_trained_target_dir)
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54 _add_data_table_entry(data_manager_dict, data_table_entry)
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5
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55
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56 cleanup_before_exit('tmp')
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57
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5
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58 def _add_data_table_entry(data_manager_dict, data_table_entry):
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59 data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
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60 data_manager_dict['data_tables']['reference_data'] = data_manager_dict['data_tables'].get('reference_data', [])
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61 data_manager_dict['data_tables']['reference_data'].append( data_table_entry )
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62 return data_manager_dict
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63
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64 def main():
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65 #Parse Command Line
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66 parser = argparse.ArgumentParser()
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3
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67 parser.add_argument('-o', '--out', help='Output file')
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68 args = parser.parse_args()
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69
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3
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70 filename = args.out
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1
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71
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72 params = from_json_string(open(filename).read())
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73 target_directory = params['output_data'][0]['extra_files_path']
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74 os.mkdir(target_directory)
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75 data_manager_dict = {}
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76
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77 sequence_id, sequence_name = get_reference_id_name(params)
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5
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78 trained_dir = get_url(params)
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79 #Fetch the FASTA
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80 download_from_GlimmerHMM(data_manager_dict, target_directory, sequence_id, sequence_name, trained_dir)
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81 #save info to json file
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82 open(filename, 'wb').write(to_json_string(data_manager_dict))
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83
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84 if __name__ == "__main__":
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85 main()
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86
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