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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
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6
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23 if motif_db == "pouya":
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24 BGZ = ['COMPBIO URL HERE',
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25 "pouya_motifs.bed.bgz", "pouya_bgz", "Pouya Encode Motifs (hg19) BGZ"]
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26 TBI = ['COMPBIO URL HERE',
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27 "pouya_motifs.bed.bgz.tbi", "pouya_tbi", "Pouya Encode Motifs (hg19) TBI"]
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28 elif motif_db == "jaspar":
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29 BGZ = ['COMPBIO URL HERE',
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30 "jaspar_jolma_motifs.bed.bgz", "jaspar_bgz", "Jaspar and Jolma Motifs (hg19) BGZ"]
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31 TBI = ['COMPBIO URL HERE',
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32 "jaspar_jolma_motifs.bed.bgz.tbi", "jaspar_tbi", "Jaspar and Jolma Motifs (hg19) TBI"]
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33 elif motif_db == "mouse":
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34 BGZ = ['COMPBIO URL HERE',
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35 "mouse_motifs.bed.bgz", "mouse_bgz", "Mouse Motifs (mm9) BGZ"]
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36 TBI = ['COMPBIO URL HERE',
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37 "mouse_motifs.bed.bgz.tbi", "mouse_tbi", "Mouse Motifs (mm9) TBI"]
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38 else:
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39 BGZ = ['http://gehlenborg.com/wp-content/uploads/motif/pouya_test_motifs.bed.bgz',
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40 "pouya_test_motifs.bed.bgz", "test_bgz", "Test Pouya Subset (hg19) BGZ"]
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41 TBI = ['http://gehlenborg.com/wp-content/uploads/motif/pouya_test_motifs.bed.bgz.tbi',
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42 "pouya_test_motifs.bed.bgz.tbi", "test_tbi", "Test Pouya Subset (hg19) TBI"]
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43
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44 bgz_reader = urllib2.urlopen( BGZ[0] )
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4
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45 bgz_data_table_entry = _stream_fasta_to_file( bgz_reader, target_directory, params,
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6
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46 BGZ[1], BGZ[2], BGZ[3] )
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4
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47 _add_data_table_entry( data_manager_dict, 'motif_databases', bgz_data_table_entry )
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48
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49 tbi_reader = urllib2.urlopen( TBI[0] )
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4
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50 tbi_data_table_entry = _stream_fasta_to_file( tbi_reader, target_directory, params,
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51 TBI[1], TBI[2], TBI[3] )
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4
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52 _add_data_table_entry( data_manager_dict, 'motif_databases', tbi_data_table_entry )
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53
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2
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54 def _add_data_table_entry( data_manager_dict, data_table, data_table_entry ):
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55 data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
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2
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56 data_manager_dict['data_tables'][data_table] = data_manager_dict['data_tables'].get( data_table, [] )
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57 data_manager_dict['data_tables'][data_table].append( data_table_entry )
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58 return data_manager_dict
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59
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5
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60 def _stream_fasta_to_file( fasta_stream, target_directory, params,
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61 fasta_base_filename, value, name, close_stream=True ):
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62 fasta_filename = os.path.join( target_directory, fasta_base_filename )
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63 fasta_writer = open( fasta_filename, 'wb+' )
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64
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65 while True:
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66 buffer = fasta_stream.read(CHUNK_SIZE)
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67 if not buffer:
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68 break
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69
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70 fasta_writer.write(buffer)
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71
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72 fasta_stream.close()
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73 fasta_writer.close()
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74
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4
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75 return dict( value=value, name=name, path=fasta_base_filename )
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0
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76
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77 def main():
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78 #Parse Command Line
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79 parser = optparse.OptionParser()
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80 parser.add_option( '-m', '--motif_db', dest='motif_db', action='store', type="string", default=None, help='motif_db' )
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81 (options, args) = parser.parse_args()
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82
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83 filename = args[0]
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84
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85 params = from_json_string( open( filename ).read() )
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86 target_directory = params[ 'output_data' ][0]['extra_files_path']
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87 os.mkdir( target_directory )
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88 data_manager_dict = {}
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89
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90 #Fetch the Motif Database
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1
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91 download_motif_databases( data_manager_dict, params, target_directory, options.motif_db )
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0
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92
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93 #save info to json file
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94 open( filename, 'wb' ).write( to_json_string( data_manager_dict ) )
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95
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96 if __name__ == "__main__": main()
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