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1 #!/usr/bin/env python
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2 # Jeremy Liu
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3 # February 2015
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4 # Adapted from Dan Blackenburg's sample data manager
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5
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6 import sys
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7 import os
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8 import tempfile
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9 import shutil
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10 import optparse
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11 import urllib2
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12 #import uuid
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13 from ftplib import FTP
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14 import tarfile
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15 import zipfile
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16 import gzip
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17 import bz2
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18
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19 from galaxy.util.json import from_json_string, to_json_string
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20
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21 CHUNK_SIZE = 2**20 #1mb
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22
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23 def download_motif_databases( data_manager_dict, params, target_directory, motif_db ):
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24
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25 # Select download URL, file name, data table name, and path using motif_db selector variable
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26 if motif_db == "encode":
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27 BGZ = ['http://compbio.med.harvard.edu/motif-enrichment/pouya_motifs.bed.bgz',
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28 "pouya_motifs.bed.bgz", "encode_bgz", "Encode Motifs (hg19) BGZ"]
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29 TBI = ['http://compbio.med.harvard.edu/motif-enrichment/pouya_motifs.bed.bgz.tbi',
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30 "pouya_motifs.bed.bgz.tbi", "encode_tbi", "Encode Motifs (hg19) TBI"]
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31 PWM = ['http://compbio.med.harvard.edu/motif-enrichment/pwms/pouya.pwms.from.seq.meme.txt',
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32 "pouya.pwms.from.seq.meme.txt", "encode_pwm", "Encode Motifs (hg19) PWM MEME"]
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33 elif motif_db == "jaspar":
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34 BGZ = ['http://compbio.med.harvard.edu/motif-enrichment/jaspar_jolma_motifs.bed.bgz',
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35 "jaspar_jolma_motifs.bed.bgz", "jaspar_bgz", "Jaspar and Jolma Motifs (hg19) BGZ"]
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36 TBI = ['http://compbio.med.harvard.edu/motif-enrichment/jaspar_jolma_motifs.bed.bgz.tbi',
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37 "jaspar_jolma_motifs.bed.bgz.tbi", "jaspar_tbi", "Jaspar and Jolma Motifs (hg19) TBI"]
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38 PWM = ['http://compbio.med.harvard.edu/motif-enrichment/pwms/jaspar.jolma.pwms.from.seq.meme.txt',
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39 "jaspar.jolma.pwms.from.seq.meme.txt", "jaspar_pwm", "Jaspar and Jolma Motifs (hg19) PWM MEME"]
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40 elif motif_db == "mouse":
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41 BGZ = ['http://compbio.med.harvard.edu/motif-enrichment/mm9_motifs_split.bed.bgz',
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42 "mm9_motifs_split.bed.bgz", "mouse_bgz", "Mouse Motifs (mm9) BGZ"]
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43 TBI = ['http://compbio.med.harvard.edu/motif-enrichment/mm9_motifs_split.bed.bgz.tbi',
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44 "mm9_motifs_split.bed.bgz.tbi", "mouse_tbi", "Mouse Motifs (mm9) TBI"]
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45 PWM = ['http://compbio.med.harvard.edu/motif-enrichment/pwms/mm9.pwms.from.seq.meme.txt',
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46 "mm9.pwms.from.seq.meme.txt", "mouse_pwm", "Mouse Motifs (mm9) PWM MEME"]
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47 else:
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48 BGZ = ['http://compbio.med.harvard.edu/motif-enrichment/pouya_test_motifs.bed.bgz',
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49 "pouya_test_motifs.bed.bgz", "test_bgz", "Test Encode Motifs (hg19) BGZ"]
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50 TBI = ['http://compbio.med.harvard.edu/motif-enrichment/pouya_test_motifs.bed.bgz.tbi',
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51 "pouya_test_motifs.bed.bgz.tbi", "test_tbi", "Test Encode Motifs (hg19) TBI"]
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52 PWM = ['http://compbio.med.harvard.edu/motif-enrichment/pwms/pouya.pwms.from.seq.meme.txt',
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53 "pouya.pwms.from.seq.meme.txt", "test_pwm", "Test Encode Motifs (hg19) PWM MEME"]
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54
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55
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56 # Save and add motif bgz file to motif_databases data table
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57 bgz_reader = urllib2.urlopen( BGZ[0] )
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58 bgz_data_table_entry = _stream_fasta_to_file( bgz_reader, target_directory, params,
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59 BGZ[1], BGZ[2], BGZ[3] )
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60 _add_data_table_entry( data_manager_dict, 'motif_databases', bgz_data_table_entry )
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61
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62 # Save and add motif tbi file to motif_databases data table
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63 tbi_reader = urllib2.urlopen( TBI[0] )
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64 tbi_data_table_entry = _stream_fasta_to_file( tbi_reader, target_directory, params,
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65 TBI[1], TBI[2], TBI[3] )
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66 _add_data_table_entry( data_manager_dict, 'motif_databases', tbi_data_table_entry )
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67
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68 # Save and add motif pwm file to motif_databases data table
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69 tbi_reader = urllib2.urlopen( PWM[0] )
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70 tbi_data_table_entry = _stream_fasta_to_file( tbi_reader, target_directory, params,
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71 PWM[1], PWM[2], PWM[3] )
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72 _add_data_table_entry( data_manager_dict, 'motif_databases', tbi_data_table_entry )
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73
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74 def _add_data_table_entry( data_manager_dict, data_table, data_table_entry ):
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75 data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
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76 data_manager_dict['data_tables'][data_table] = data_manager_dict['data_tables'].get( data_table, [] )
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77 data_manager_dict['data_tables'][data_table].append( data_table_entry )
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78 return data_manager_dict
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79
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80 def _stream_fasta_to_file( fasta_stream, target_directory, params,
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81 fasta_base_filename, value, name, close_stream=True ):
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82 fasta_filename = os.path.join( target_directory, fasta_base_filename )
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83 fasta_writer = open( fasta_filename, 'wb+' )
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84
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85 while True:
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86 buffer = fasta_stream.read(CHUNK_SIZE)
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87 if not buffer:
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88 break
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89
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90 fasta_writer.write(buffer)
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91
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92 fasta_stream.close()
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93 fasta_writer.close()
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94
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95 return dict( value=value, name=name, path=fasta_base_filename )
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96
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97 def main():
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98 #Parse Command Line
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99 parser = optparse.OptionParser()
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100 parser.add_option( '-m', '--motif_db', dest='motif_db', action='store', type="string", default=None, help='motif_db' )
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101 (options, args) = parser.parse_args()
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102
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103 filename = args[0]
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104
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105 params = from_json_string( open( filename ).read() )
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106 target_directory = params[ 'output_data' ][0]['extra_files_path']
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107 os.mkdir( target_directory )
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108 data_manager_dict = {}
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109
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110 #Fetch the Motif Database
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111 download_motif_databases( data_manager_dict, params, target_directory, options.motif_db )
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112
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113 #save info to json file
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114 open( filename, 'wb' ).write( to_json_string( data_manager_dict ) )
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115
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116 if __name__ == "__main__": main()
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