Mercurial > repos > yating-l > multi_fasta_glimmer_hmm

annotate fetch_reference_data.py @ 7:0f39f40ef695 draft

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planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 59eb9b27c7382ae4736eb7425615e4b575757378
author yating-l
date Wed, 03 May 2017 15:15:36 -0400
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7
0f39f40ef695 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 59eb9b27c7382ae4736eb7425615e4b575757378
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1 #!/usr/bin/env python
0f39f40ef695 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 59eb9b27c7382ae4736eb7425615e4b575757378
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2 # ref: https://galaxyproject.org/admin/tools/data-managers/how-to/define/
0f39f40ef695 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 59eb9b27c7382ae4736eb7425615e4b575757378
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0f39f40ef695 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 59eb9b27c7382ae4736eb7425615e4b575757378
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4 import sys
0f39f40ef695 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 59eb9b27c7382ae4736eb7425615e4b575757378
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5 import os
0f39f40ef695 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 59eb9b27c7382ae4736eb7425615e4b575757378
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6 import tempfile
0f39f40ef695 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 59eb9b27c7382ae4736eb7425615e4b575757378
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7 import shutil
0f39f40ef695 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 59eb9b27c7382ae4736eb7425615e4b575757378
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8 import argparse
0f39f40ef695 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 59eb9b27c7382ae4736eb7425615e4b575757378
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9 import urllib2
0f39f40ef695 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 59eb9b27c7382ae4736eb7425615e4b575757378
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10 import tarfile
0f39f40ef695 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 59eb9b27c7382ae4736eb7425615e4b575757378
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12 from galaxy.util.json import from_json_string, to_json_string
0f39f40ef695 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 59eb9b27c7382ae4736eb7425615e4b575757378
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14 CHUNK_SIZE = 2**20 #1mb
0f39f40ef695 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 59eb9b27c7382ae4736eb7425615e4b575757378
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0f39f40ef695 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 59eb9b27c7382ae4736eb7425615e4b575757378
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16 def cleanup_before_exit(tmp_dir):
0f39f40ef695 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 59eb9b27c7382ae4736eb7425615e4b575757378
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17 if tmp_dir and os.path.exists(tmp_dir):
0f39f40ef695 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 59eb9b27c7382ae4736eb7425615e4b575757378
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18 shutil.rmtree(tmp_dir)
0f39f40ef695 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 59eb9b27c7382ae4736eb7425615e4b575757378
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20 def stop_err(msg):
0f39f40ef695 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 59eb9b27c7382ae4736eb7425615e4b575757378
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21 sys.stderr.write(msg)
0f39f40ef695 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 59eb9b27c7382ae4736eb7425615e4b575757378
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22 sys.exit(1)
0f39f40ef695 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 59eb9b27c7382ae4736eb7425615e4b575757378
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24 def get_reference_id_name(params):
0f39f40ef695 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 59eb9b27c7382ae4736eb7425615e4b575757378
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25 genome_id = params['param_dict']['genome_id']
0f39f40ef695 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 59eb9b27c7382ae4736eb7425615e4b575757378
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26 genome_name = params['param_dict']['genome_name']
0f39f40ef695 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 59eb9b27c7382ae4736eb7425615e4b575757378
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27 return genome_id, genome_name
0f39f40ef695 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 59eb9b27c7382ae4736eb7425615e4b575757378
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29 def download_from_GlimmerHMM(data_manager_dict, params, target_directory, sequence_id, sequence_name ):
0f39f40ef695 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 59eb9b27c7382ae4736eb7425615e4b575757378
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30 GlimmerHMM_DOWNLOAD_URL = 'ftp://ccb.jhu.edu/pub/software/glimmerhmm/GlimmerHMM-3.0.4.tar.gz'
0f39f40ef695 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 59eb9b27c7382ae4736eb7425615e4b575757378
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31 GlimmerHMM_TRAINED_DIR = os.path.join('GlimmerHMM', 'trained_dir', sequence_id)
0f39f40ef695 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 59eb9b27c7382ae4736eb7425615e4b575757378
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32 with tarfile.open('GlimmerHMM-3.0.4.tar', mode='r:*') as tar:
0f39f40ef695 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 59eb9b27c7382ae4736eb7425615e4b575757378
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33 subdir = [
0f39f40ef695 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 59eb9b27c7382ae4736eb7425615e4b575757378
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34 tarinfo for tarinfo in tar.getmembers()
0f39f40ef695 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 59eb9b27c7382ae4736eb7425615e4b575757378
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35 if sequence_id in tarinfo.name
0f39f40ef695 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 59eb9b27c7382ae4736eb7425615e4b575757378
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36 ]
0f39f40ef695 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 59eb9b27c7382ae4736eb7425615e4b575757378
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37 tar.extractall(members=subdir)
0f39f40ef695 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 59eb9b27c7382ae4736eb7425615e4b575757378
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38 glimmerhmm_trained_target_dir = os.path.join(target_directory, sequence_id)
0f39f40ef695 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 59eb9b27c7382ae4736eb7425615e4b575757378
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39 shutil.copytree(GlimmerHMM_TRAINED_DIR, glimmerhmm_trained_target_dir)
0f39f40ef695 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 59eb9b27c7382ae4736eb7425615e4b575757378
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40 data_table_entry = dict(value=sequence_id, name=sequence_name, path=glimmerhmm_trained_target_dir)
0f39f40ef695 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 59eb9b27c7382ae4736eb7425615e4b575757378
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41 _add_data_table_entry(data_manager_dict, data_table_entry)
0f39f40ef695 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 59eb9b27c7382ae4736eb7425615e4b575757378
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43 cleanup_before_exit(GlimmerHMM_TRAINED_DIR)
0f39f40ef695 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 59eb9b27c7382ae4736eb7425615e4b575757378
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45 def _add_data_table_entry( data_manager_dict, data_table_entry ):
0f39f40ef695 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 59eb9b27c7382ae4736eb7425615e4b575757378
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46 data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
0f39f40ef695 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 59eb9b27c7382ae4736eb7425615e4b575757378
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47 data_manager_dict['data_tables']['reference_data'] = data_manager_dict['data_tables'].get('reference_data', [])
0f39f40ef695 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 59eb9b27c7382ae4736eb7425615e4b575757378
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48 data_manager_dict['data_tables']['reference_data'].append( data_table_entry )
0f39f40ef695 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 59eb9b27c7382ae4736eb7425615e4b575757378
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49 return data_manager_dict
0f39f40ef695 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 59eb9b27c7382ae4736eb7425615e4b575757378
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51 REFERENCE_SOURCE_TO_DOWNLOAD = dict(glimmerhmm=download_from_GlimmerHMM)
0f39f40ef695 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 59eb9b27c7382ae4736eb7425615e4b575757378
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53 def main():
0f39f40ef695 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 59eb9b27c7382ae4736eb7425615e4b575757378
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54 #Parse Command Line
0f39f40ef695 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 59eb9b27c7382ae4736eb7425615e4b575757378
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55 parser = argparse.ArgumentParser()
0f39f40ef695 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 59eb9b27c7382ae4736eb7425615e4b575757378
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56 args = parser.parse_args()
0f39f40ef695 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 59eb9b27c7382ae4736eb7425615e4b575757378
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58 filename = args[0]
0f39f40ef695 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 59eb9b27c7382ae4736eb7425615e4b575757378
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0f39f40ef695 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 59eb9b27c7382ae4736eb7425615e4b575757378
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60 params = from_json_string(open(filename).read())
0f39f40ef695 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 59eb9b27c7382ae4736eb7425615e4b575757378
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61 target_directory = params['output_data'][0]['extra_files_path']
0f39f40ef695 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 59eb9b27c7382ae4736eb7425615e4b575757378
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62 os.mkdir(target_directory)
0f39f40ef695 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 59eb9b27c7382ae4736eb7425615e4b575757378
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63 data_manager_dict = {}
0f39f40ef695 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 59eb9b27c7382ae4736eb7425615e4b575757378
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65 sequence_id, sequence_name = get_reference_id_name(params)
0f39f40ef695 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 59eb9b27c7382ae4736eb7425615e4b575757378
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66
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67 #Fetch the FASTA
0f39f40ef695 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 59eb9b27c7382ae4736eb7425615e4b575757378
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68 REFERENCE_SOURCE_TO_DOWNLOAD[params['param_dict']['file_path']](data_manager_dict, params, target_directory, sequence_id, sequence_name)
0f39f40ef695 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 59eb9b27c7382ae4736eb7425615e4b575757378
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70 #save info to json file
0f39f40ef695 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 59eb9b27c7382ae4736eb7425615e4b575757378
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71 open(filename, 'wb').write(to_json_string(data_manager_dict))
0f39f40ef695 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 59eb9b27c7382ae4736eb7425615e4b575757378
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73 if __name__ == "__main__":
0f39f40ef695 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 59eb9b27c7382ae4736eb7425615e4b575757378
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74 main()
0f39f40ef695 planemo upload for repository https://github.com/remimarenco/multi_fasta_glimmerhmm.git commit 59eb9b27c7382ae4736eb7425615e4b575757378
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