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1 #!/usr/bin/env python
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2 #Dan Blankenberg
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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 optparse
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9 import urllib2
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10 #import uuid
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11 from ftplib import FTP
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12 import tarfile
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13 import zipfile
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14 import gzip
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15 import bz2
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16
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17 from galaxy.util.json import from_json_string, to_json_string
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18
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19 CHUNK_SIZE = 2**20 #1mb
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20
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21 def download_motif_databases( data_manager_dict, params, target_directory, motif_db ):
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22 TEST_DOWNLOAD_URL = 'http://gehlenborg.com/wp-content/uploads/motif/pouya_test_motifs.bed.bgz'
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23 #TO DO: Add tbi file
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24
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25 url = TEST_DOWNLOAD_URL
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26 fasta_reader = urllib2.urlopen( url )
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27
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28 data_table_entry = _stream_fasta_to_file( fasta_reader, target_directory, params )
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2
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29 _add_data_table_entry( data_manager_dict, 'motif_databases', data_table_entry )
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30
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2
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31 def _add_data_table_entry( data_manager_dict, data_table, data_table_entry ):
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32 data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
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2
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33 data_manager_dict['data_tables'][data_table] = data_manager_dict['data_tables'].get( data_table, [] )
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34 data_manager_dict['data_tables'][data_table].append( data_table_entry )
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35 return data_manager_dict
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36
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37 def _stream_fasta_to_file( fasta_stream, target_directory, params, close_stream=True ):
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38 fasta_base_filename = "pouya_test_motifs.bed.bgz"
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39 fasta_filename = os.path.join( target_directory, fasta_base_filename )
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40 fasta_writer = open( fasta_filename, 'wb+' )
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41
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42 while True:
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43 buffer = fasta_stream.read(CHUNK_SIZE)
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44 if not buffer:
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45 break
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46
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47 fasta_writer.write(buffer)
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48
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49 fasta_stream.close()
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50 fasta_writer.close()
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51
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52 return dict( value="test", name="Test Pouya Subset (hg19)", path=fasta_base_filename )
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53
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54 def main():
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55 #Parse Command Line
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56 parser = optparse.OptionParser()
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57 parser.add_option( '-m', '--motif_db', dest='motif_db', action='store', type="string", default=None, help='motif_db' )
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58 (options, args) = parser.parse_args()
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59
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60 filename = args[0]
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61
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62 params = from_json_string( open( filename ).read() )
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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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66
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67 #Fetch the Motif Database
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68 download_motif_databases( data_manager_dict, params, target_directory, options.motif_db )
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69
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70 #save info to json file
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71 open( filename, 'wb' ).write( to_json_string( data_manager_dict ) )
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72
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73 if __name__ == "__main__": main()
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